Fix divide by zero in sinefit

Might fix the problem Mark noticed where turn-off transients
are erroneously matching the drop that follows startup transients.

.gitignore

@@ -1,3 +1,6 @@
+oldprep
+newprep
+*.dat
 build/
 *.pyc
 dist/

Makefile

@@ -1,5 +1,78 @@
-all:
-	@echo "Try 'make install'"
+#URL="http://bucket.mit.edu:8080/nilmdb"
+URL="http://localhost/nilmdb"
+
+all: test
+
+test:
+ifeq ($(INSIDE_EMACS), t)
+	@make test_sinefit
+else
+	@echo 'No test suite for nilmtools.  Try "make install"'
+endif
+
+test_pipewatch:
+	nilmtools/pipewatch.py -t 3 "seq 10 20" "seq 20 30"
+
+test_trainola:
+	-nilmtool -u http://bucket/nilmdb remove -s min -e max \
+		/sharon/prep-a-matches
+	nilmtools/trainola.py "$$(cat extras/trainola-test-param.js)"
+
+test_trainola2:
+	-nilmtool -u http://bucket/nilmdb remove -s min -e max \
+		/sharon/prep-a-matches
+	nilmtools/trainola.py "$$(cat extras/trainola-test-param-2.js)"
+
+test_trainola3:
+	-nilmtool -u "http://bucket/nilmdb" destroy -R /test/jim
+	nilmtool -u "http://bucket/nilmdb" create /test/jim uint8_3
+	nilmtools/trainola.py "$$(cat extras/trainola-test-param-3.js)"
+	nilmtool -u "http://bucket/nilmdb" extract /test/jim -s min -e max
+
+test_cleanup:
+	nilmtools/cleanup.py -e extras/cleanup.cfg
+	nilmtools/cleanup.py extras/cleanup.cfg
+
+test_insert:
+	nilmtools/insert.py --skip --file --dry-run /foo/bar ~/data/20130311T2100.prep1.gz ~/data/20130311T2100.prep1.gz ~/data/20130311T2200.prep1.gz
+
+test_copy:
+	nilmtools/copy_wildcard.py -U "http://nilmdb.com/bucket/" -D /lees*
+
+/tmp/raw.dat:
+	octave --eval 'fs = 8000;' \
+	--eval 't = (0:fs*10)*2*pi*60/fs;' \
+	--eval 'raw = transpose([sin(t); 0.3*sin(3*t)+sin(t)]);' \
+	--eval 'save("-ascii","/tmp/raw.dat","raw");'
+
+test_prep: /tmp/raw.dat
+	-nilmtool destroy -R /test/raw
+	-nilmtool destroy -R /test/sinefit
+	-nilmtool destroy -R /test/prep
+	nilmtool create /test/raw float32_2
+	nilmtool create /test/sinefit float32_3
+	nilmtool create /test/prep float32_8
+	nilmtool insert -s '@0' -t -r 8000 /test/raw /tmp/raw.dat
+	nilmtools/sinefit.py -a 0.5 -c 1 -s '@0' -e '@5000000' /test/raw /test/sinefit
+	nilmtools/prep.py -c 2 /test/raw /test/sinefit /test/prep
+	nilmtools/prep.py -c 2 /test/raw /test/sinefit /test/prep
+	nilmtool extract -s min -e max /test/prep | head -20
+
+test_sinefit:
+	make install >/dev/null 2>&1
+	-nilmtool destroy -R /test/sinefit
+	nilmtool create /test/sinefit float32_3
+	nilmtools/sinefit.py -c 5 -s '2013/03/25 09:11:00' \
+	-e '2013/03/25 10:11:00' /sharon/raw /test/sinefit
+	nilmtool extract -s min -e max /test/sinefit | head -20
+
+test_decimate:
+	-@nilmtool destroy /lees-compressor/no-leak/raw/4 || true
+	-@nilmtool destroy /lees-compressor/no-leak/raw/16 || true
+	-@nilmtool create /lees-compressor/no-leak/raw/4 float32_18 || true
+	-@nilmtool create /lees-compressor/no-leak/raw/16 float32_18 || true
+	time python nilmtools/decimate.py -s '2013-02-04 18:10:00' -e '2013-02-04 18:11:00' /lees-compressor/no-leak/raw/1 /lees-compressor/no-leak/raw/4
+	python nilmtools/decimate.py -s '2013-02-04 18:10:00' -e '2013-02-04 18:11:00' /lees-compressor/no-leak/raw/4 /lees-compressor/no-leak/raw/16
 
 version:
 	python setup.py version
@@ -21,4 +94,4 @@ clean::
 gitclean::
 	git clean -dXf
 
-.PHONY: all version dist sdist install clean gitclean
+.PHONY: all version dist sdist install clean gitclean test

README.txt

@@ -6,9 +6,22 @@ Prerequisites:
 
   # Runtime and build environments
   sudo apt-get install python2.7 python2.7-dev python-setuptools
+  sudo apt-get install python-numpy python-scipy python-daemon
 
-  nilmdb (1.3.1+)
+  nilmdb (1.8.5+)
 
 Install:
 
   python setup.py install
+
+Building new tools:
+
+  The tools in this package are meant to be installed with
+  "python setup.py install".  If you want to make a new one,
+  an easier way to develop would be to first install this package,
+  and then copy a specific script like "src/sinefit.py" to a new
+  location, and modify it as desired.
+
+  To add a tool to the package, place it in "src/" and add the
+  appropriate configuration to "setup.py".
+

extras/cleanup.cfg

@@ -0,0 +1,22 @@
+[/lees-compressor/no-leak/prep]
+keep = 2d
+rate = 60
+
+[*/raw]
+keep = 2d
+
+[*/something]
+rate = 10
+
+[*/sinefit]
+keep = 1w
+decimated = False
+
+[/test/raw]
+keep = 0.01d
+
+[/test/sinefit]
+keep = 0.01d
+
+[/test/prep]
+keep = 0.01d

extras/sample-cron-scripts/capture.sh

@@ -0,0 +1,10 @@
+#!/bin/bash
+
+# Start the ethstream capture using nilm-pipewatch
+
+# Bail out on errors
+set -e
+
+nilm-pipewatch --daemon --lock "/tmp/nilmdb-capture.lock" --timeout 30 \
+    "ethstream -a 192.168.1.209 -n 9 -r 8000 -N" \
+    "nilm-insert -m 10 -r 8000 --live /sharon/raw"

extras/sample-cron-scripts/cleanup.cfg

@@ -0,0 +1,9 @@
+[/sharon/prep-*]
+keep = 1y
+
+[/sharon/raw]
+keep = 2w
+
+[/sharon/sinefit]
+keep = 1y
+decimated = false

extras/sample-cron-scripts/crontab

@@ -0,0 +1,15 @@
+# Install this by running "crontab crontab" (will replace existing crontab)
+
+SHELL=/bin/bash
+PATH=/usr/local/bin:/usr/local/sbin:/usr/bin:/usr/sbin:/bin:/sbin
+
+# m h dom mon dow cmd
+
+# Run NilmDB processing every 5 minutes
+*/5 * * * * chronic /home/nilm/data/process.sh
+
+# Try frequently restarting the capture process in case it died
+*/5 * * * * chronic /home/nilm/data/capture.sh
+
+# Run fsck at startup
+@reboot chronic nilmdb-fsck --fix --no-data /home/nilm/data/db/

extras/sample-cron-scripts/process.sh

@@ -0,0 +1,32 @@
+#!/bin/bash
+# Run all necessary processing on NilmDB data.
+
+# Bail out on errors
+set -e
+
+# Ensure only one copy of this code runs at a time:
+LOCKFILE="/tmp/nilmdb-process.lock"
+exec 99>"$LOCKFILE"
+if ! flock -n -x 99 ; then
+    echo "NilmDB processing already running, giving up..."
+    exit 0
+fi
+trap 'rm -f "$LOCKFILE"' 0
+
+# redirect stdout/stderr to log, but keep it on the console too
+exec >  >(tee /home/nilm/data/process.log)
+exec 2> >(tee -a /home/nilm/data/process.log >&2)
+
+echo "sinefit on phase A voltage"
+nilm-sinefit -c 5 /sharon/raw /sharon/sinefit
+
+echo "prep on A, B, C with appropriate rotations"
+nilm-prep -c 1 -r 0 /sharon/raw /sharon/sinefit /sharon/prep-a
+nilm-prep -c 2 -r 120 /sharon/raw /sharon/sinefit /sharon/prep-b
+nilm-prep -c 3 -r 240 /sharon/raw /sharon/sinefit /sharon/prep-c
+
+echo "decimate raw and prep data"
+nilm-decimate-auto /sharon/raw /sharon/prep*
+
+echo "run cleanup"
+nilm-cleanup --yes /home/nilm/data/cleanup.cfg

extras/trainola-test-param-2.js

@@ -0,0 +1,29 @@
+{ "columns" : [ { "index" : 0, "name" : "P1" },
+                { "index" : 1, "name" : "Q1" },
+                { "index" : 2, "name" : "P3" } ],
+  "stream" : "/sharon/prep-a",
+  "url" : "http://bucket.mit.edu/nilmdb",
+  "dest_stream" : "/sharon/prep-a-matches",
+  "start" : 1365153062643133.5,
+  "end"   : 1365168814443575.5,
+  "exemplars" : [ { "columns" : [ { "index" : 0,
+                                    "name" : "P1"
+                                  } ],
+                    "dest_column" : 0,
+                    "end" : 1365073657682000,
+                    "name" : "Turn ON",
+                    "start" : 1365073654321000,
+                    "stream" : "/sharon/prep-a",
+                    "url" : "http://bucket.mit.edu/nilmdb"
+                  },
+                  { "columns" : [ { "index" : 2, "name" : "P3" },
+                                  { "index" : 0, "name" : "P1" } ],
+                    "dest_column" : 1,
+                    "end" : 1365176528818000,
+                    "name" : "Type 2 turn ON",
+                    "start" : 1365176520030000,
+                    "stream" : "/sharon/prep-a",
+                    "url" : "http://bucket.mit.edu/nilmdb"
+                  }
+                ]
+}

extras/trainola-test-param-3.js

@@ -0,0 +1,40 @@
+{
+    "url": "http://bucket/nilmdb",
+    "stream": "/sharon/prep-a",
+    "dest_stream": "/test/jim",
+    "start": 1364184839901599,
+    "end": 1364184942407610.2,
+
+    "columns": [ { "index": 0, "name": "P1" } ],
+
+    "exemplars": [
+        {
+            "name": "A - True DBL Freezer ON",
+            "dest_column": 0,
+            "url": "http://bucket/nilmdb",
+            "stream": "/sharon/prep-a",
+            "columns": [ { "index": 0, "name": "P1" } ],
+            "start": 1365277707649000,
+            "end": 1365277710705000
+        },
+        {
+            "name": "A - Boiler 1 Fan OFF",
+            "dest_column": 1,
+            "url": "http://bucket/nilmdb",
+            "stream": "/sharon/prep-a",
+            "columns": [ { "index": 0, "name": "P1" } ],
+            "start": 1364188370735000,
+            "end": 1364188373819000
+        },
+        {
+            "name": "A - True DBL Freezer OFF",
+            "dest_column": 2,
+            "url": "http://bucket/nilmdb",
+            "stream": "/sharon/prep-a",
+            "columns": [ { "index": 0, "name": "P1" } ],
+            "start": 1365278087982000,
+            "end": 1365278089340000
+        }
+   ]
+}
+

extras/trainola-test-param.js

@@ -0,0 +1,31 @@
+{ "url": "http://bucket.mit.edu/nilmdb",
+  "dest_stream": "/sharon/prep-a-matches",
+  "stream": "/sharon/prep-a",
+  "start": 1366111383280463,
+  "end": 1366126163457797,
+  "columns": [ { "name": "P1", "index": 0 },
+               { "name": "Q1", "index": 1 },
+               { "name": "P3", "index": 2 } ],
+  "exemplars": [
+      { "name": "Boiler Pump ON",
+        "url": "http://bucket.mit.edu/nilmdb",
+        "stream": "/sharon/prep-a",
+        "start": 1366260494269078,
+        "end": 1366260608185031,
+        "dest_column": 0,
+        "columns": [ { "name": "P1", "index": 0 },
+                     { "name": "Q1", "index": 1 }
+                   ]
+      },
+      { "name": "Boiler Pump OFF",
+        "url": "http://bucket.mit.edu/nilmdb",
+        "stream": "/sharon/prep-a",
+        "start": 1366260864215764,
+        "end": 1366260870882998,
+        "dest_column": 1,
+        "columns": [ { "name": "P1", "index": 0 },
+                     { "name": "Q1", "index": 1 }
+                   ]
+      }
+  ]
+}

nilmtools/cleanup.py

@@ -0,0 +1,257 @@
+#!/usr/bin/python
+
+from nilmdb.utils.printf import *
+from nilmdb.utils.time import (parse_time, timestamp_to_human,
+                               timestamp_to_seconds, seconds_to_timestamp)
+from nilmdb.utils.diskusage import human_size
+from nilmdb.utils.interval import Interval
+import nilmdb.client
+import nilmdb.client.numpyclient
+import nilmtools
+import argparse
+import ConfigParser
+import sys
+import collections
+import fnmatch
+import re
+
+def warn(msg, *args):
+    fprintf(sys.stderr, "warning: " + msg + "\n", *args)
+
+class TimePeriod(object):
+    _units = { 'h': ('hour',  60*60),
+               'd': ('day',   60*60*24),
+               'w': ('week',  60*60*24*7),
+               'm': ('month', 60*60*24*30),
+               'y': ('year',  60*60*24*365) }
+
+    def __init__(self, val):
+        for u in self._units:
+            if val.endswith(u):
+                self.unit = self._units[u][0]
+                self.scale = self._units[u][1]
+                self.count = float(val[:-len(u)])
+                break
+        else:
+            raise ValueError("unknown units: " + units)
+
+    def seconds(self):
+        return self.count * self.scale
+
+    def describe_seconds(self, seconds):
+        count = seconds / self.scale
+        units = self.unit if count == 1 else (self.unit + "s")
+        if count == int(count):
+            return sprintf("%d %s", count, units)
+        else:
+            return sprintf("%.2f %s", count, units)
+
+    def __str__(self):
+        return self.describe_seconds(self.seconds())
+
+class StreamCleanupConfig(object):
+    def __init__(self, info):
+        self.path = info[0]
+        self.layout = info[1]
+        if info[4] != 0 and info[5] != 0:
+            self.rate = info[4] / timestamp_to_seconds(info[5])
+        else:
+            self.rate = None
+        self.keep = None
+        self.clean_decimated = True
+        self.decimated_from = None
+        self.also_clean_paths = []
+
+def main(argv = None):
+    parser = argparse.ArgumentParser(
+        formatter_class = argparse.RawDescriptionHelpFormatter,
+        version = nilmtools.__version__,
+        description = """\
+    Clean up old data from streams using a configuration file to specify
+    which data to remove.
+
+    The format of the config file is as follows:
+
+      [/stream/path]
+      keep = 3w         # keep up to 3 weeks of data
+      rate = 8000       # optional, used for the --estimate option
+      decimated = false # whether to delete decimated data too (default true)
+
+      [*/prep]
+      keep = 3.5m       # or 2520h or 105d or 15w or 0.29y
+
+    The suffix for 'keep' is 'h' for hours, 'd' for days, 'w' for weeks,
+    'm' for months, or 'y' for years.
+
+    Streams paths may include wildcards.  If a path is matched by more than
+    one config section, data from the last config section counts.
+
+    Decimated streams (paths containing '~decim-') are treated specially:
+      - They don't match wildcards
+      - When deleting data from a parent stream, data is also deleted
+        from its decimated streams, unless decimated=false
+
+    Rate is optional and is only used for the --estimate option.
+    """)
+    parser.add_argument("-u", "--url", action="store",
+                        default="http://localhost/nilmdb/",
+                        help="NilmDB server URL (default: %(default)s)")
+    parser.add_argument("-y", "--yes", action="store_true",
+                        default = False,
+                        help="Actually remove the data (default: no)")
+    parser.add_argument("-e", "--estimate", action="store_true",
+                        default = False,
+                        help="Estimate how much disk space will be used")
+    parser.add_argument("configfile", type=argparse.FileType('r'),
+                        help="Configuration file")
+    args = parser.parse_args(argv)
+
+    # Parse config file
+    config = ConfigParser.RawConfigParser()
+    config.readfp(args.configfile)
+
+    # List all streams
+    client = nilmdb.client.Client(args.url)
+    streamlist = client.stream_list(extended = True)
+
+    # Create config objects
+    streams = collections.OrderedDict()
+    for s in streamlist:
+        streams[s[0]] = StreamCleanupConfig(s)
+        m = re.search(r"^(.*)~decim-[0-9]+$", s[0])
+        if m:
+            streams[s[0]].decimated_from = m.group(1)
+
+    # Build up configuration
+    for section in config.sections():
+        matched = False
+        for path in streams.iterkeys():
+            # Decimated streams only allow exact matches
+            if streams[path].decimated_from and path != section:
+                continue
+            if not fnmatch.fnmatch(path, section):
+                continue
+            matched = True
+            options = config.options(section)
+
+            # Keep period (days, weeks, months, years)
+            if 'keep' in options:
+                streams[path].keep = TimePeriod(config.get(section, 'keep'))
+                options.remove('keep')
+
+            # Rate
+            if 'rate' in options:
+                streams[path].rate = config.getfloat(section, 'rate')
+                options.remove('rate')
+
+            # Decimated
+            if 'decimated' in options:
+                val = config.getboolean(section, 'decimated')
+                streams[path].clean_decimated = val
+                options.remove('decimated')
+
+            for leftover in options:
+                warn("option '%s' for '%s' is unknown", leftover, section)
+
+        if not matched:
+            warn("config for '%s' did not match any existing streams", section)
+
+    # List all decimated streams in the parent stream's info
+    for path in streams.keys():
+        src = streams[path].decimated_from
+        if src and src in streams:
+            if streams[src].clean_decimated:
+                streams[src].also_clean_paths.append(path)
+                del streams[path]
+
+    # Warn about streams that aren't getting cleaned up
+    for path in streams.keys():
+        if streams[path].keep is None or streams[path].keep.seconds() < 0:
+            warn("no config for existing stream '%s'", path)
+            del streams[path]
+
+    if args.estimate:
+        # Estimate disk usage
+        total = 0
+        for path in streams.keys():
+            rate = streams[path].rate
+            if not rate or rate < 0:
+                warn("unable to estimate disk usage for stream '%s' because "
+                     "the data rate is unknown", path)
+                continue
+            printf("%s:\n", path)
+            layout = streams[path].layout
+            dtype = nilmdb.client.numpyclient.layout_to_dtype(layout)
+            per_row = dtype.itemsize
+            per_sec = per_row * rate
+            printf("%17s: %s per row, %s rows per second\n",
+                   "base rate",
+                   human_size(per_row),
+                   round(rate,1))
+            printf("%17s: %s per hour, %s per day\n",
+                   "base size",
+                   human_size(per_sec * 3600),
+                   human_size(per_sec * 3600 * 24))
+
+            # If we'll be cleaning up decimated data, add an
+            # estimation for how much room decimated data takes up.
+            if streams[path].clean_decimated:
+                d_layout = "float32_" + str(3*(int(layout.split('_')[1])))
+                d_dtype = nilmdb.client.numpyclient.layout_to_dtype(d_layout)
+                # Assume the decimations will be a factor of 4
+                # sum_{k=0..inf} (rate / (n^k)) * d_dtype.itemsize
+                d_per_row = d_dtype.itemsize
+                factor = 4.0
+                d_per_sec = d_per_row * (rate / factor) * (1 / (1 - (1/factor)))
+                per_sec += d_per_sec
+                printf("%17s: %s per hour, %s per day\n",
+                       "with decimation",
+                       human_size(per_sec * 3600),
+                       human_size(per_sec * 3600 * 24))
+
+            keep = per_sec * streams[path].keep.seconds()
+            printf("%17s: %s\n\n",
+                   "keep " + str(streams[path].keep), human_size(keep))
+            total += keep
+        printf("Total estimated disk usage for these streams:\n")
+        printf("  %s\n", human_size(total))
+        raise SystemExit(0)
+
+    # Do the cleanup
+    for path in streams:
+        printf("%s: keep %s\n", path, streams[path].keep)
+
+        # Figure out the earliest timestamp we should keep.
+        intervals = [ Interval(start, end) for (start, end) in
+                      reversed(list(client.stream_intervals(path))) ]
+        total = 0
+        keep = seconds_to_timestamp(streams[path].keep.seconds())
+        for i in intervals:
+            total += i.end - i.start
+            if total <= keep:
+                continue
+            remove_before = i.start + (total - keep)
+            break
+        else:
+            printf("  nothing to do (only %s of data present)\n",
+                   streams[path].keep.describe_seconds(
+                       timestamp_to_seconds(total)))
+            continue
+        printf("  removing data before %s\n", timestamp_to_human(remove_before))
+        # Clean in reverse order.  Since we only use the primary stream and not
+        # the decimated streams to figure out which data to remove, removing
+        # the primary stream last means that we might recover more nicely if
+        # we are interrupted and restarted.
+        clean_paths = list(reversed(streams[path].also_clean_paths)) + [ path ]
+        for p in clean_paths:
+            printf("  removing from %s\n", p)
+            if args.yes:
+                client.stream_remove(p, None, remove_before)
+
+    # All done
+    if not args.yes:
+        printf("Note: specify --yes to actually perform removals\n")
+    return
+
+if __name__ == "__main__":
+    main()

nilmtools/copy_one.py

@@ -0,0 +1,44 @@
+#!/usr/bin/python
+
+# This is called copy_one instead of copy to avoid name conflicts with
+# the Python standard library.
+
+import nilmtools.filter
+import nilmdb.client
+from nilmdb.client.numpyclient import NumpyClient
+import numpy as np
+import sys
+
+def main(argv = None):
+    f = nilmtools.filter.Filter()
+    parser = f.setup_parser("Copy a stream")
+    parser.add_argument('-n', '--nometa', action='store_true',
+                        help="Don't copy or check metadata")
+
+    # Parse arguments
+    try:
+        args = f.parse_args(argv)
+    except nilmtools.filter.MissingDestination as e:
+        print "Source is %s (%s)" % (e.src.path, e.src.layout)
+        print "Destination %s doesn't exist" % (e.dest.path)
+        print "You could make it with a command like:"
+        print "  nilmtool -u %s create %s %s" % (e.dest.url,
+                                                 e.dest.path, e.src.layout)
+        raise SystemExit(1)
+
+    # Copy metadata
+    if not args.nometa:
+        meta = f.client_src.stream_get_metadata(f.src.path)
+        f.check_dest_metadata(meta)
+
+    # Copy all rows of data using the faster Numpy interfaces
+    extractor = NumpyClient(f.src.url).stream_extract_numpy
+    inserter = NumpyClient(f.dest.url).stream_insert_numpy_context
+    for i in f.intervals():
+        print "Processing", i.human_string()
+        with inserter(f.dest.path, i.start, i.end) as insert_ctx:
+            for data in extractor(f.src.path, i.start, i.end):
+                insert_ctx.insert(data)
+
+if __name__ == "__main__":
+    main()

nilmtools/copy_wildcard.py

@@ -0,0 +1,74 @@
+#!/usr/bin/python
+
+# Copy streams between NilmDB servers with wildcards
+
+import nilmtools.filter
+import nilmtools.copy_one
+import nilmdb.client
+import argparse
+import fnmatch
+
+def main(argv = None):
+    f = nilmtools.filter.Filter()
+    # Reuse filter's parser, since it handles most options we need.
+    parser = f.setup_parser(description = """\
+    Copy all streams matching the given wildcard from one host to another.
+
+    Example: %(prog)s -u http://host1/nilmdb -U http://host2/nilmdb /sharon/*
+    """, skip_paths = True)
+    parser.add_argument('-n', '--nometa', action='store_true',
+                        help="Don't copy or check metadata")
+    parser.add_argument("path", action="store", nargs="+",
+                        help='Wildcard paths to copy')
+    args = parser.parse_args(argv)
+
+    # Verify arguments
+    if args.dest_url is None:
+        parser.error("must provide both source and destination URL")
+    client_src = nilmdb.client.Client(args.url)
+    client_dest = nilmdb.client.Client(args.dest_url)
+    if client_src.geturl() == client_dest.geturl():
+        parser.error("source and destination URL must be different")
+    print "Source URL:", client_src.geturl()
+    print "  Dest URL:", client_dest.geturl()
+
+    # Find matching streams
+    matched = []
+    for path in args.path:
+        matched.extend([s for s in client_src.stream_list(extended = True)
+                        if fnmatch.fnmatch(s[0], path)
+                        and s not in matched])
+
+    # Create destination streams if they don't exist
+    for stream in matched:
+        src = nilmtools.filter.StreamInfo(client_src.geturl(), stream)
+        dest = nilmtools.filter.get_stream_info(client_dest, src.path)
+        if not dest:
+            print "Creating destination stream", src.path
+            client_dest.stream_create(src.path, src.layout)
+
+    # Copy them all by running the "copy" tool as if it were
+    # invoked from the command line.
+    for stream in matched:
+        new_argv = ["--url", client_src.geturl(),
+                     "--dest-url", client_dest.geturl() ]
+        if args.start:
+            new_argv.extend(["--start", "@" + repr(args.start)])
+        if args.end:
+            new_argv.extend(["--end", "@" + repr(args.end)])
+        if args.dry_run:
+            new_argv.extend(["--dry-run"])
+        if args.nometa:
+            new_argv.extend(["--nometa"])
+        if args.force_metadata:
+            new_argv.extend(["--force-metadata"])
+        new_argv.extend([stream[0], stream[0]])
+        try:
+            nilmtools.copy_one.main(new_argv)
+        except SystemExit as e:
+            # Ignore SystemExit which could be raised on --dry-run
+            if e.code != 0:
+                raise
+
+if __name__ == "__main__":
+    main()

nilmtools/decimate.py

@@ -0,0 +1,85 @@
+#!/usr/bin/python
+
+import nilmtools.filter
+import nilmdb.client
+import numpy as np
+import operator
+
+def main(argv = None):
+    f = nilmtools.filter.Filter()
+    parser = f.setup_parser("Decimate a stream")
+    group = parser.add_argument_group("Decimate options")
+    group.add_argument('-f', '--factor', action='store', default=4, type=int,
+                       help='Decimation factor (default: %(default)s)')
+
+    # Parse arguments
+    try:
+        args = f.parse_args(argv)
+    except nilmtools.filter.MissingDestination as e:
+        # If no destination, suggest how to create it by figuring out
+        # a recommended layout.
+        src = e.src
+        dest = e.dest
+        print "Source is %s (%s)" % (src.path, src.layout)
+        print "Destination %s doesn't exist" % (dest.path)
+        if "decimate_source" in f.client_src.stream_get_metadata(src.path):
+            rec = src.layout
+        elif 'int32' in src.layout_type or 'float64' in src.layout_type:
+            rec = 'float64_' + str(src.layout_count * 3)
+        else:
+            rec = 'float32_' + str(src.layout_count * 3)
+        print "You could make it with a command like:"
+        print "  nilmtool -u %s create %s %s" % (e.dest.url,
+                                                 e.dest.path, rec)
+        raise SystemExit(1)
+
+    if not (args.factor >= 2):
+        raise Exception("factor needs to be 2 or more")
+
+    f.check_dest_metadata({ "decimate_source": f.src.path,
+                            "decimate_factor": args.factor })
+
+    # If source is decimated, we have to decimate a bit differently
+    if "decimate_source" in f.client_src.stream_get_metadata(args.srcpath):
+        again = True
+    else:
+        again = False
+    f.process_numpy(decimate, args = (args.factor, again))
+
+def decimate(data, interval, args, insert_function, final):
+    """Decimate data"""
+    (factor, again) = args
+    (n, m) = data.shape
+
+    # Figure out which columns to use as the source for mean, min, and max,
+    # depending on whether this is the first decimation or we're decimating
+    # again.  Note that we include the timestamp in the means.
+    if again:
+        c = (m - 1) // 3
+        # e.g. c = 3
+        # ts mean1 mean2 mean3 min1 min2 min3 max1 max2 max3
+        mean_col = slice(0, c + 1)
+        min_col = slice(c + 1, 2 * c + 1)
+        max_col = slice(2 * c + 1, 3 * c + 1)
+    else:
+        mean_col = slice(0, m)
+        min_col = slice(1, m)
+        max_col = slice(1, m)
+
+    # Discard extra rows that aren't a multiple of factor
+    n = n // factor * factor
+    data = data[:n,:]
+
+    # Reshape it into 3D so we can process 'factor' rows at a time
+    data = data.reshape(n // factor, factor, m)
+
+    # Fill the result
+    out = np.c_[ np.mean(data[:,:,mean_col], axis=1),
+                 np.min(data[:,:,min_col], axis=1),
+                 np.max(data[:,:,max_col], axis=1) ]
+
+    insert_function(out)
+    return n
+
+if __name__ == "__main__":
+    main()

nilmtools/decimate_auto.py

@@ -0,0 +1,98 @@
+#!/usr/bin/python
+
+import nilmtools.filter
+import nilmtools.decimate
+import nilmdb.client
+import argparse
+import fnmatch
+
+def main(argv = None):
+    parser = argparse.ArgumentParser(
+        formatter_class = argparse.RawDescriptionHelpFormatter,
+        version = nilmtools.__version__,
+        description = """\
+    Automatically create multiple decimations from a single source
+    stream, continuing until the last decimated level contains fewer
+    than 500 points total.
+
+    Wildcards and multiple paths are accepted.  Decimated paths are
+    ignored when matching wildcards.
+    """)
+    parser.add_argument("-u", "--url", action="store",
+                        default="http://localhost/nilmdb/",
+                        help="NilmDB server URL (default: %(default)s)")
+    parser.add_argument("-f", "--factor", action="store", default=4, type=int,
+                        help='Decimation factor (default: %(default)s)')
+    parser.add_argument("-F", "--force-metadata", action="store_true",
+                        default = False,
+                        help="Force metadata changes if the dest "
+                        "doesn't match")
+    parser.add_argument("path", action="store", nargs='+',
+                        help='Path of base stream')
+    args = parser.parse_args(argv)
+
+    # Pull out info about the base stream
+    client = nilmdb.client.Client(args.url)
+
+    # Find list of paths to process
+    streams = [ unicode(s[0]) for s in client.stream_list() ]
+    streams = [ s for s in streams if "~decim-" not in s ]
+    paths = []
+    for path in args.path:
+        new = fnmatch.filter(streams, unicode(path))
+        if not new:
+            print "error: no stream matched path:", path
+            raise SystemExit(1)
+        paths.extend(new)
+
+    for path in paths:
+        do_decimation(client, args, path)
+
+def do_decimation(client, args, path):
+    print "Decimating", path
+    info = nilmtools.filter.get_stream_info(client, path)
+    if not info:
+        raise Exception("path " + path + " not found")
+
+    meta = client.stream_get_metadata(path)
+    if "decimate_source" in meta:
+        print "Stream", path, "was decimated from", meta["decimate_source"]
+        print "You need to pass the base stream instead"
+        raise SystemExit(1)
+
+    # Figure out the type we should use for decimated streams
+    if 'int32' in info.layout_type or 'float64' in info.layout_type:
+        decimated_type = 'float64_' + str(info.layout_count * 3)
+    else:
+        decimated_type = 'float32_' + str(info.layout_count * 3)
+
+    # Now do the decimations until we have few enough points
+    factor = 1
+    while True:
+        print "Level", factor, "decimation has", info.rows, "rows"
+        if info.rows <= 500:
+            break
+        factor *= args.factor
+        new_path = "%s~decim-%d" % (path, factor)
+
+        # Create the stream if needed
+        new_info = nilmtools.filter.get_stream_info(client, new_path)
+        if not new_info:
+            print "Creating stream", new_path
+            client.stream_create(new_path, decimated_type)
+
+        # Run the decimation as if it were run from the commandline
+        new_argv = [ "-u", args.url,
+                     "-f", str(args.factor) ]
+        if args.force_metadata:
+            new_argv.extend([ "--force-metadata" ])
+        new_argv.extend([info.path, new_path])
+        nilmtools.decimate.main(new_argv)
+
+        # Update info using the newly decimated stream
+        info = nilmtools.filter.get_stream_info(client, new_path)
+
+    return
+
+if __name__ == "__main__":
+    main()

nilmtools/filter.py

@@ -1,66 +1,389 @@
 #!/usr/bin/python
 
-import nilmdb.client
-from nilmdb.utils.printf import *
-from nilmdb.utils.time import parse_time, format_time
+from __future__ import absolute_import
 
+import nilmdb.client
+from nilmdb.client import Client
+from nilmdb.client.numpyclient import NumpyClient
+from nilmdb.utils.printf import *
+from nilmdb.utils.time import (parse_time, timestamp_to_human,
+                               timestamp_to_seconds)
+from nilmdb.utils.interval import Interval
+
+import nilmtools
+
+import itertools
 import time
 import sys
 import re
 import argparse
+import numpy as np
+import cStringIO
+import functools
+
+class ArgumentError(Exception):
+    pass
+
+class MissingDestination(Exception):
+    def __init__(self, args, src, dest):
+        self.parsed_args = args
+        self.src = src
+        self.dest = dest
+        Exception.__init__(self, "destination path " + dest.path + " not found")
+
+class StreamInfo(object):
+    def __init__(self, url, info):
+        self.url = url
+        self.info = info
+        try:
+            self.path = info[0]
+            self.layout = info[1]
+            self.layout_type = self.layout.split('_')[0]
+            self.layout_count = int(self.layout.split('_')[1])
+            self.total_count = self.layout_count + 1
+            self.timestamp_min = info[2]
+            self.timestamp_max = info[3]
+            self.rows = info[4]
+            self.seconds = nilmdb.utils.time.timestamp_to_seconds(info[5])
+        except IndexError, TypeError:
+            pass
+
+    def string(self, interhost):
+        """Return stream info as a string.  If interhost is true,
+        include the host URL."""
+        if interhost:
+            return sprintf("[%s] ", self.url) + str(self)
+        return str(self)
+
+    def __str__(self):
+        """Return stream info as a string."""
+        return sprintf("%s (%s), %.2fM rows, %.2f hours",
+                       self.path, self.layout, self.rows / 1e6,
+                       self.seconds / 3600.0)
+
+def get_stream_info(client, path):
+    """Return a StreamInfo object about the given path, or None if it
+    doesn't exist"""
+    streams = client.stream_list(path, extended = True)
+    if len(streams) != 1:
+        return None
+    return StreamInfo(client.geturl(), streams[0])
+
+# Filter processing for a single interval of data.
+def process_numpy_interval(interval, extractor, inserter, warn_rows,
+                           function, args = None):
+    """For the given 'interval' of data, extract data, process it
+    through 'function', and insert the result.
+
+    'extractor' should be a function like NumpyClient.stream_extract_numpy
+    but with the the interval 'start' and 'end' as the only parameters,
+    e.g.:
+       extractor = functools.partial(NumpyClient.stream_extract_numpy,
+                                     src_path, layout = l, maxrows = m)
+
+    'inserter' should be a function like NumpyClient.stream_insert_context
+    but with the interval 'start' and 'end' as the only parameters, e.g.:
+       inserter = functools.partial(NumpyClient.stream_insert_context,
+                                    dest_path)
+
+    If 'warn_rows' is not None, print a warning to stdout when the
+    number of unprocessed rows exceeds this amount.
+
+    See process_numpy for details on 'function' and 'args'.
+    """
+    if args is None:
+        args = []
+
+    with inserter(interval.start, interval.end) as insert_ctx:
+        insert_func = insert_ctx.insert
+        old_array = np.array([])
+        for new_array in extractor(interval.start, interval.end):
+            # If we still had old data left, combine it
+            if old_array.shape[0] != 0:
+                array = np.vstack((old_array, new_array))
+            else:
+                array = new_array
+
+            # Pass the data to the user provided function
+            processed = function(array, interval, args, insert_func, False)
+
+            # Send any pending data that the user function inserted
+            insert_ctx.send()
+
+            # Save the unprocessed parts
+            if processed >= 0:
+                old_array = array[processed:]
+            else:
+                raise Exception(
+                    sprintf("%s return value %s must be >= 0",
+                            str(function), str(processed)))
+
+            # Warn if there's too much data remaining
+            if warn_rows is not None and old_array.shape[0] > warn_rows:
+                printf("warning: %d unprocessed rows in buffer\n",
+                       old_array.shape[0])
+
+        # Last call for this contiguous interval
+        if old_array.shape[0] != 0:
+            processed = function(old_array, interval, args,
+                                 insert_func, True)
+            if processed != old_array.shape[0]:
+                # Truncate the interval we're inserting at the first
+                # unprocessed data point.  This ensures that
+                # we'll not miss any data when we run again later.
+                insert_ctx.update_end(old_array[processed][0])
+
+def example_callback_function(data, interval, args, insert_func, final):
+    """Example of the signature for the function that gets passed
+    to process_numpy_interval.
+
+    'data': array of data to process -- may be empty
+
+    'interval': overall interval we're processing (but not necessarily
+    the interval of this particular chunk of data)
+
+    'args': opaque arguments passed to process_numpy
+
+    'insert_func': function to call in order to insert array of data.
+    Should be passed a 2-dimensional array of data to insert.
+    Data timestamps must be within the provided interval.
+
+    'final': True if this is the last bit of data for this
+    contiguous interval, False otherwise.
+
+    Return value of 'function' is the number of data rows processed.
+    Unprocessed data will be provided again in a subsequent call
+    (unless 'final' is True).
+
+    If unprocessed data remains after 'final' is True, the interval
+    being inserted will be ended at the timestamp of the first
+    unprocessed data point.
+    """
+    raise NotImplementedError("example_callback_function does nothing")
 
 class Filter(object):
 
-    def __init__(self, description = "Filter data"):
-        self.args = None
-        self._client = None
-        self.parse_args(description)
+    def __init__(self, parser_description = None):
+        self._parser = None
+        self._client_src = None
+        self._client_dest = None
+        self._using_client = False
+        self.src = None
+        self.dest = None
+        self.start = None
+        self.end = None
+        self._interhost = False
+        self._force_metadata = False
+        if parser_description is not None:
+            self.setup_parser(parser_description)
+            self.parse_args()
 
-    def parse_args(self, description):
+    @property
+    def client_src(self):
+        if self._using_client:
+            raise Exception("Filter client is in use; make another")
+        return self._client_src
+
+    @property
+    def client_dest(self):
+        if self._using_client:
+            raise Exception("Filter client is in use; make another")
+        return self._client_dest
+
+    def setup_parser(self, description = "Filter data", skip_paths = False):
         parser = argparse.ArgumentParser(
-            description = description,
-            formatter_class = argparse.RawDescriptionHelpFormatter)
-        parser.add_argument("-u", "--url", action="store",
-                            default="http://localhost:12380/",
+            formatter_class = argparse.RawDescriptionHelpFormatter,
+            version = nilmtools.__version__,
+            description = description)
+        group = parser.add_argument_group("General filter arguments")
+        group.add_argument("-u", "--url", action="store",
+                           default="http://localhost/nilmdb/",
                            help="Server URL (default: %(default)s)")
-        parser.add_argument("srcpath", action="store",
+        group.add_argument("-U", "--dest-url", action="store",
+                           help="Destination server URL "
+                           "(default: same as source)")
+        group.add_argument("-D", "--dry-run", action="store_true",
+                           default = False,
+                           help="Just print intervals that would be "
+                           "processed")
+        group.add_argument("-F", "--force-metadata", action="store_true",
+                           default = False,
+                           help="Force metadata changes if the dest "
+                           "doesn't match")
+        group.add_argument("-s", "--start",
+                           metavar="TIME", type=self.arg_time,
+                           help="Starting timestamp for intervals "
+                           "(free-form, inclusive)")
+        group.add_argument("-e", "--end",
+                           metavar="TIME", type=self.arg_time,
+                           help="Ending timestamp for intervals "
+                           "(free-form, noninclusive)")
+        if not skip_paths:
+            # Individual filter scripts might want to add these arguments
+            # themselves, to include multiple sources in a different order
+            # (for example).  "srcpath" and "destpath" arguments must exist,
+            # though.
+            group.add_argument("srcpath", action="store",
                                help="Path of source stream, e.g. /foo/bar")
-        parser.add_argument("destpath", action="store",
+            group.add_argument("destpath", action="store",
                                help="Path of destination stream, e.g. /foo/bar")
-        self.args = parser.parse_args()
+        self._parser = parser
+        return parser
 
-        self._client = nilmdb.client.Client(args.url)
+    def set_args(self, url, dest_url, srcpath, destpath, start, end,
+                 parsed_args = None, quiet = True):
+        """Set arguments directly from parameters"""
+        if dest_url is None:
+            dest_url = url
+        if url != dest_url:
+            self._interhost = True
 
-        if args.srcpath == args.destpath:
-            raise Exception("source and destination path must be different")
+        self._client_src = Client(url)
+        self._client_dest = Client(dest_url)
 
-        # Open and print info about the streams
-        def stream_info_string(info):
-            return sprintf("%s (%s), %.2fM rows, %.2f hours\n",
-                           info[0], info[1], info[4] / 1e6, info[5] / 3600)
+        if (not self._interhost) and (srcpath == destpath):
+            raise ArgumentError("source and destination path must be different")
 
-        src = self._client.stream_list(args.srcpath, extended = True)
-        if len(src) != 1:
-            raise Exception("source path " + args.srcpath + " not found")
-        print "Source:", stream_info_string(src[0])
+        # Open the streams
+        self.src = get_stream_info(self._client_src, srcpath)
+        if not self.src:
+            raise ArgumentError("source path " + srcpath + " not found")
 
-        dest = self._client.stream_list(args.destpath, extended = True)
-        if len(dest) != 1:
-            raise Exception("destination path " + args.destpath + " not found")
-        print "  Dest:", stream_info_string(dest[0])
+        self.dest = get_stream_info(self._client_dest, destpath)
+        if not self.dest:
+            raise MissingDestination(parsed_args, self.src,
+                                     StreamInfo(dest_url, [destpath]))
+
+        self.start = start
+        self.end = end
+
+        # Print info
+        if not quiet:
+            print "Source:", self.src.string(self._interhost)
+            print "  Dest:", self.dest.string(self._interhost)
+
+    def parse_args(self, argv = None):
+        """Parse arguments from a command line"""
+        args = self._parser.parse_args(argv)
+
+        self.set_args(args.url, args.dest_url, args.srcpath, args.destpath,
+                      args.start, args.end, quiet = False, parsed_args = args)
+
+        self._force_metadata = args.force_metadata
+        if args.dry_run:
+            for interval in self.intervals():
+                print interval.human_string()
+            raise SystemExit(0)
+        return args
 
     def intervals(self):
         """Generate all the intervals that this filter should process"""
-        for i in self._client.stream_intervals(
-            args.srcpath, diffpath = args.destpath):
-            yield i
+        self._using_client = True
 
-def main():
+        if self._interhost:
+            # Do the difference ourselves
+            s_intervals = ( Interval(start, end)
+                            for (start, end) in
+                            self._client_src.stream_intervals(
+                                self.src.path,
+                                start = self.start, end = self.end) )
+            d_intervals = ( Interval(start, end)
+                            for (start, end) in
+                            self._client_dest.stream_intervals(
+                                self.dest.path,
+                                start = self.start, end = self.end) )
+            intervals = nilmdb.utils.interval.set_difference(s_intervals,
+                                                             d_intervals)
+        else:
+            # Let the server do the difference for us
+            intervals = ( Interval(start, end)
+                          for (start, end) in
+                          self._client_src.stream_intervals(
+                              self.src.path, diffpath = self.dest.path,
+                              start = self.start, end = self.end) )
+        # Optimize intervals: join intervals that are adjacent
+        for interval in nilmdb.utils.interval.optimize(intervals):
+            yield interval
+        self._using_client = False
+
+    # Misc helpers
+    @staticmethod
+    def arg_time(toparse):
+        """Parse a time string argument"""
+        try:
+            return nilmdb.utils.time.parse_time(toparse)
+        except ValueError as e:
+            raise argparse.ArgumentTypeError(sprintf("%s \"%s\"",
+                                                     str(e), toparse))
+
+    def check_dest_metadata(self, data):
+        """See if the metadata jives, and complain if it doesn't.  For
+        each key in data, if the stream contains the key, it must match
+        values.  If the stream does not contain the key, it is created."""
+        metadata = self._client_dest.stream_get_metadata(self.dest.path)
+        if not self._force_metadata:
+            for key in data:
+                wanted = data[key]
+                if not isinstance(wanted, basestring):
+                    wanted = str(wanted)
+                val = metadata.get(key, wanted)
+                # Force UTF-8 encoding for comparison and display
+                wanted = wanted.encode('utf-8')
+                val = val.encode('utf-8')
+                key = key.encode('utf-8')
+                if val != wanted and self.dest.rows > 0:
+                    m =  "Metadata in destination stream:\n"
+                    m += "  %s = %s\n" % (key, val)
+                    m += "doesn't match desired data:\n"
+                    m += "  %s = %s\n" % (key, wanted)
+                    m += "Refusing to change it.  To prevent this error, "
+                    m += "change or delete the metadata with nilmtool,\n"
+                    m += "remove existing data from the stream, or "
+                    m += "retry with --force-metadata."
+                    raise Exception(m)
+        # All good -- write the metadata in case it's not already there
+        self._client_dest.stream_update_metadata(self.dest.path, data)
+
+    # The main filter processing method.
+    def process_numpy(self, function, args = None, rows = 100000,
+                      intervals = None):
+        """Calls process_numpy_interval for each interval that currently
+        exists in self.src, but doesn't exist in self.dest.  It will
+        process the data in chunks as follows:
+
+        For each chunk of data, call 'function' with a Numpy array
+        corresponding to the data.  The data is converted to a Numpy
+        array in chunks of 'rows' rows at a time.
+
+        If 'intervals' is not None, process those intervals instead of
+        the default list.
+
+        'function' should be defined with the same interface as
+        nilmtools.filter.example_callback_function.  See the
+        documentation of that for details.  'args' are passed to
+        'function'.
+        """
+        extractor = NumpyClient(self.src.url).stream_extract_numpy
+        inserter = NumpyClient(self.dest.url).stream_insert_numpy_context
+
+        extractor_func = functools.partial(extractor, self.src.path,
+                                           layout = self.src.layout,
+                                           maxrows = rows)
+        inserter_func = functools.partial(inserter, self.dest.path)
+
+        for interval in (intervals or self.intervals()):
+            print "Processing", interval.human_string()
+            process_numpy_interval(interval, extractor_func, inserter_func,
+                                   rows * 3, function, args)
+
+def main(argv = None):
     # This is just a dummy function; actual filters can use the other
     # functions to prepare stuff, and then do something with the data.
     f = Filter()
-    for interval in f.intervals():
-        print "Generic filter: need to handle interval:", interval
+    parser = f.setup_parser()
+    args = f.parse_args(argv)
+    for i in f.intervals():
+        print "Generic filter: need to handle", i.human_string()
 
 if __name__ == "__main__":
     main()

nilmtools/insert.py

@@ -2,80 +2,173 @@
 
 import nilmdb.client
 from nilmdb.utils.printf import *
-from nilmdb.utils.time import parse_time, format_time
+from nilmdb.utils.time import (parse_time, timestamp_to_human,
+                               timestamp_to_seconds, seconds_to_timestamp,
+                               rate_to_period, now as time_now)
 
+import nilmtools
 import time
 import sys
 import re
 import argparse
 import subprocess
+import textwrap
 
 class ParseError(Exception):
     def __init__(self, filename, error):
         msg = filename + ": " + error
         super(ParseError, self).__init__(msg)
 
-def parse_args():
-    parser = argparse.ArgumentParser(description = """\
-    Insert data from ethstream, either live (using the system time as a
-    reference) or prerecorded (using comments in the file as a reference).
+def parse_args(argv = None):
+    parser = argparse.ArgumentParser(
+        formatter_class = argparse.RawDescriptionHelpFormatter,
+        version = nilmtools.__version__,
+        description = textwrap.dedent("""\
+    Insert large amount of data from an external source like ethstream.
 
-    The data is assumed to have been recorded at the specified rate.
-    Small discrepencies between the accumulated timestamps and the
-    reference time are ignored; larger discrepencies cause gaps to be
-    created in the stream.  Overlapping data returns an error.
-    """, formatter_class = argparse.RawDescriptionHelpFormatter)
+    This code tracks two timestamps:
+
+    (1) The 'data' timestamp is the precise timestamp corresponding to
+        a particular row of data, and is the timestamp that gets
+        inserted into the database.  It increases by 'data_delta' for
+        every row of input.
+
+        'data_delta' can come from one of two sources.  If '--delta'
+        is specified, it is pulled from the first column of data.  If
+        '--rate' is specified, 'data_delta' is set to a fixed value of
+        (1 / rate).
+
+    (2) The 'clock' timestamp is the less precise timestamp that gives
+        the absolute time.  It can come from two sources.  If '--live'
+        is specified, it is pulled directly from the system clock.  If
+        '--file' is specified, it is extracted from the input filename
+        every time a new file is opened for read, and from comments
+        that appear in the file.
+
+    Small discrepencies between 'data' and 'clock' are ignored.  If
+    the 'data' timestamp ever differs from the 'clock' timestamp by
+    more than 'max_gap' seconds:
+
+    - If 'data' is running behind, there is a gap in the data, so it
+      is stepped forward to match 'clock'.
+
+    - If 'data' is running ahead, there is overlap in the data, and an
+      error is raised.  If '--skip' is specified, the current file
+      is skipped instead of raising an error.
+    """))
     parser.add_argument("-u", "--url", action="store",
-                        default="http://localhost:12380/",
+                        default="http://localhost/nilmdb/",
                         help="NilmDB server URL (default: %(default)s)")
-    parser.add_argument("-r", "--rate", action="store", default=8000, type=float,
-                        help="Data rate in Hz (default: %(default)s)")
-    parser.add_argument("-l", "--live", action="store_true",
-                        help="Live capture; use system time to verify rate")
-    parser.add_argument("path", action="store",
+    group = parser.add_argument_group("Misc options")
+    group.add_argument("-D", "--dry-run", action="store_true",
+                       help="Parse files, but don't insert any data")
+    group.add_argument("-s", "--skip", action="store_true",
+                       help="Skip files if the data would overlap")
+    group.add_argument("-m", "--max-gap", action="store", default=10.0,
+                       metavar="SEC", type=float,
+                       help="Max discrepency between clock and data "
+                       "timestamps (default: %(default)s)")
+
+    group = parser.add_argument_group("Data timestamp delta")
+    exc = group.add_mutually_exclusive_group()
+    exc.add_argument("-r", "--rate", action="store", default=8000.0,
+                     type=float,
+                     help="Data_delta is constant 1/RATE "
+                     "(default: %(default)s Hz)")
+    exc.add_argument("-d", "--delta", action="store_true",
+                     help="Data_delta is the first number in each line")
+
+    group = parser.add_argument_group("Clock timestamp source")
+    exc = group.add_mutually_exclusive_group()
+    exc.add_argument("-l", "--live", action="store_true",
+                     help="Use live system time for clock timestamp")
+    exc.add_argument("-f", "--file", action="store_true", default=True,
+                     help="Use filename or comments for clock timestamp")
+    group.add_argument("-o", "--offset-filename", metavar="SEC",
+                       action="store", default=-3600.0, type=float,
+                       help="Offset to add to filename timestamps "
+                       "(default: %(default)s)")
+    group.add_argument("-O", "--offset-comment", metavar="SEC",
+                       action="store", default=0.0, type=float,
+                       help="Offset to add to comment timestamps "
+                       "(default: %(default)s)")
+
+    group = parser.add_argument_group("Database path")
+    group.add_argument("path", action="store",
                        help="Path of stream, e.g. /foo/bar")
-    parser.add_argument("infile", type=argparse.FileType('r'), nargs='*',
-                        default=[sys.stdin], help="Input files (default: stdin)")
-    args = parser.parse_args()
+
+    group = parser.add_argument_group("Input files")
+    group.add_argument("infile", type=argparse.FileType('r'), nargs='*',
+                       default=[sys.stdin],
+                       help="Input files (default: stdin)")
+
+    args = parser.parse_args(argv)
 
     printf("     Stream path: %s\n", args.path)
-    printf("  Data rate: %s Hz\n", repr(args.rate))
+
+    printf("  Data timestamp: ")
+    if args.delta:
+        printf("delta on each input line\n")
+    else:
+        printf("fixed rate %s Hz\n", repr(args.rate))
+
+    printf(" Clock timestamp: ")
+    if args.live:
+        printf("live system clock\n")
+    else:
+        printf("from filenames and comments\n")
+        printf(" Filename offset: %s seconds\n", repr(args.offset_filename))
+        printf("  Comment offset: %s seconds\n", repr(args.offset_comment))
+
+    printf("         Max gap: %s seconds\n", repr(args.max_gap))
+    if args.dry_run:
+        printf("Dry run (no data will be inserted)\n")
 
     return args
 
-def main(args = None):
-    if args is None:
-        args = parse_args()
+def main(argv = None):
+    args = parse_args(argv)
 
     client = nilmdb.client.Client(args.url)
 
-    # Local copies to save dictionary lookups
-    live = args.live
-
     # data_ts is the timestamp that we'll use for the current line
     data_ts_base = 0
     data_ts_inc = 0
-    data_ts_step = 1.0 / args.rate
+    data_ts_rate = args.rate
+    data_ts_delta = 0
+    def get_data_ts():
+        if args.delta:
+            return data_ts_base + data_ts_delta
+        else:
+            return data_ts_base + rate_to_period(data_ts_rate,
+                                                 data_ts_inc)
 
     # clock_ts is the imprecise "real" timestamp (from the filename,
-    # comments, or or system clock)
+    # comments, or system clock)
     clock_ts = None
 
     def print_clock_updated():
-        printf("Clock time updated to %s\n", format_time(clock_ts))
+        printf("Clock timestamp updated to %s\n", timestamp_to_human(clock_ts))
         if data_ts_base != 0:
-            diff = data_ts - clock_ts
+            diff = get_data_ts() - clock_ts
             if diff >= 0:
-                printf("  (data timestamp ahead by %.6f sec)\n", diff)
+                printf("  (data timestamp ahead by %.6f sec)\n",
+                       timestamp_to_seconds(diff))
             else:
-                printf("  (data timestamp behind by %.6f sec)\n", -diff)
+                printf("  (data timestamp behind by %.6f sec)\n",
+                       timestamp_to_seconds(-diff))
+
+    offset_filename = seconds_to_timestamp(args.offset_filename)
+    offset_comment = seconds_to_timestamp(args.offset_comment)
+    max_gap = seconds_to_timestamp(args.max_gap)
 
     with client.stream_insert_context(args.path) as stream:
         for f in args.infile:
             filename = f.name
             printf("Processing %s\n", filename)
 
-            # If the filename ends in .gz, open it with gzcat instead.
+            # If the filename ends in .gz, re-open it with gzip to
+            # decompress.
             if filename.endswith(".gz"):
                 p = subprocess.Popen(["gzip", "-dc"],
                                      stdin = f, stdout = subprocess.PIPE)
@@ -86,7 +179,7 @@ def main(args = None):
                 # Subtract 1 hour because files are created at the end
                 # of the hour.  Hopefully, we'll be able to use
                 # internal comments and this value won't matter anyway.
-                clock_ts = parse_time(filename).totimestamp() - 3600
+                clock_ts = parse_time(filename) + offset_filename
                 print_clock_updated()
             except ValueError:
                 pass
@@ -95,7 +188,15 @@ def main(args = None):
 
             # Read each line
             for line in f:
-                data_ts = data_ts_base + data_ts_inc * data_ts_step
+                # Once in a while a line might be truncated, if we're
+                # at the end of a file.  Ignore it, but if we ignore
+                # too many, bail out.
+                if line[-1] != '\n':
+                    truncated_lines += 1
+                    if truncated_lines > 3:
+                        raise ParseError(filename, "too many short lines")
+                    printf("Ignoring short line in %s\n", filename)
+                    continue
 
                 # If no content other than the newline, skip it
                 if len(line) <= 1:
@@ -104,41 +205,57 @@ def main(args = None):
                 # If line starts with a comment, look for a timestamp
                 if line[0] == '#':
                     try:
-                        clock_ts = parse_time(line[1:]).totimestamp()
+                        clock_ts = parse_time(line[1:]) + offset_comment
                         print_clock_updated()
                     except ValueError:
                         pass
                     continue
 
+                # If --delta mode, increment data_ts_delta by the
+                # delta from the file.
+                if args.delta:
+                    try:
+                        (delta, line) = line.split(None, 1)
+                        data_ts_delta += float(delta)
+                    except ValueError:
+                        raise ParseError(filename, "can't parse delta")
+
+                # Calculate data_ts for this row
+                data_ts = get_data_ts()
+
                 # If inserting live, use clock timestamp
-                if live:
-                    clock_ts = time.time()
+                if args.live:
+                    clock_ts = time_now()
 
                 # If we have a real timestamp, compare it to the data
                 # timestamp, and make sure things match up.
                 if clock_ts is not None:
-                    if (data_ts - 10) > clock_ts:
+                    if (data_ts - max_gap) > clock_ts:
                         # Accumulated line timestamps are in the future.
                         # If we were to set data_ts=clock_ts, we'd create
                         # an overlap, so we have to just bail out here.
                         err = sprintf("Data is coming in too fast: data time "
                                       "is %s but clock time is only %s",
-                                      format_time(data_ts),
-                                      format_time(clock_ts))
+                                      timestamp_to_human(data_ts),
+                                      timestamp_to_human(clock_ts))
+                        if args.skip:
+                            printf("%s\n", err)
+                            printf("Skipping the remainder of this file\n")
+                            break
                         raise ParseError(filename, err)
 
-                    if (data_ts + 10) < clock_ts:
+                    if (data_ts + max_gap) < clock_ts:
                         # Accumulated line timetamps are in the past.  We
                         # can just skip some time and leave a gap in the
                         # data.
                         if data_ts_base != 0:
                             printf("Skipping data timestamp forward from "
                                    "%s to %s to match clock time\n",
-                                   format_time(data_ts),
-                                   format_time(clock_ts))
+                                   timestamp_to_human(data_ts),
+                                   timestamp_to_human(clock_ts))
                         stream.finalize()
                         data_ts_base = data_ts = clock_ts
-                        data_ts_inc = 0
+                        data_ts_inc = data_ts_delta = 0
 
                     # Don't use this clock time anymore until we update it
                     clock_ts = None
@@ -146,21 +263,12 @@ def main(args = None):
                 if data_ts_base == 0:
                     raise ParseError(filename, "No idea what timestamp to use")
 
-                # This line is legit, so increment timestamp
+                # This line is legit, so increment timestamp (for --rate)
                 data_ts_inc += 1
 
-                # Once in a while a line might be truncated, if we're at
-                # the end of a file.  Ignore it, but if we ignore too many,
-                # bail out.
-                if line[-1] != '\n':
-                    truncated_lines += 1
-                    if truncated_lines > 3:
-                        raise ParseError(filename, "too many short lines")
-                    printf("Ignoring short line in %s\n", filename)
-                    continue
-
                 # Insert it
-                stream.insert("%.6f %s" % (data_ts, line))
+                if not args.dry_run:
+                    stream.insert("%d %s" % (data_ts, line))
     print "Done"
 
 if __name__ == "__main__":

nilmtools/math.py

@@ -0,0 +1,111 @@
+#!/usr/bin/python
+
+# Miscellaenous useful mathematical functions
+from nilmdb.utils.printf import *
+from numpy import *
+from scipy import *
+
+def sfit4(data, fs):
+    """(A, f0, phi, C) = sfit4(data, fs)
+
+    Compute 4-parameter (unknown-frequency) least-squares fit to
+    sine-wave data, according to IEEE Std 1241-2010 Annex B
+
+    Input:
+      data  vector of input samples
+      fs    sampling rate (Hz)
+
+    Output:
+      Parameters [A, f0,  phi, C] to fit the equation
+        x[n] = A * sin(f0/fs * 2 * pi * n + phi) + C
+      where n is sample number.  Or, as a function of time:
+        x(t) = A * sin(f0 * 2 * pi * t + phi) + C
+
+    by Jim Paris
+    (Verified to match sfit4.m)
+    """
+    N = len(data)
+    t = linspace(0, (N-1) / float(fs), N)
+
+    ## Estimate frequency using FFT (step b)
+    Fc = fft(data)
+    F = abs(Fc)
+    F[0] = 0   # eliminate DC
+
+    # Find pair of spectral lines with largest amplitude:
+    # resulting values are in F(i) and F(i+1)
+    i = argmax(F[0:int(N/2)] + F[1:int(N/2+1)])
+
+    # Interpolate FFT to get a better result (from Markus [B37])
+    try:
+        U1 = real(Fc[i])
+        U2 = real(Fc[i+1])
+        V1 = imag(Fc[i])
+        V2 = imag(Fc[i+1])
+        n = 2 * pi / N
+        ni1 = n * i
+        ni2 = n * (i+1)
+        K = ((V2-V1)*sin(ni1) + (U2-U1)*cos(ni1)) / (U2-U1)
+        Z1 = V1 * (K - cos(ni1)) / sin(ni1) + U1
+        Z2 = V2 * (K - cos(ni2)) / sin(ni2) + U2
+        i = arccos((Z2*cos(ni2) - Z1*cos(ni1)) / (Z2-Z1)) / n
+    except Exception:
+        # Just go with the biggest FFT peak
+        i = argmax(F[0:int(N/2)])
+
+    # Convert to Hz
+    f0 = i * float(fs) / N
+
+    # Fit it.  We'll catch exceptions here and just returns zeros
+    # if something fails with the least squares fit, etc.
+    try:
+        # first guess for A0, B0 using 3-parameter fit (step c)
+        s = zeros(3)
+        w = 2*pi*f0
+
+        # Now iterate 7 times (step b, plus 6 iterations of step i)
+        for idx in range(7):
+            D = c_[cos(w*t), sin(w*t), ones(N),
+                  -s[0] * t * sin(w*t) + s[1] * t * cos(w*t) ] # eqn B.16
+            s = linalg.lstsq(D, data)[0] # eqn B.18
+            w = w + s[3]	# update frequency estimate
+
+        ## Extract results
+        A = sqrt(s[0]*s[0] + s[1]*s[1]) # eqn B.21
+        f0 = w / (2*pi)
+        phi = arctan2(s[0], s[1]) # eqn B.22 (flipped for sin instead of cos)
+        C = s[2]
+        return (A, f0, phi, C)
+    except Exception as e:
+        # something broke down; just return zeros
+        return (0, 0, 0, 0)
+
+def peak_detect(data, delta = 0.1):
+    """Simple min/max peak detection algorithm, taken from my code
+    in the disagg.m from the 10-8-5 paper.
+
+    Returns an array of peaks: each peak is a tuple
+      (n, p, is_max)
+    where n is the row number in 'data', and p is 'data[n]',
+    and is_max is True if this is a maximum, False if it's a minimum,
+    """
+    peaks = [];
+    cur_min = (None, inf)
+    cur_max = (None, -inf)
+    lookformax = False
+    for (n, p) in enumerate(data):
+        if p > cur_max[1]:
+            cur_max = (n, p)
+        if p < cur_min[1]:
+            cur_min = (n, p)
+        if lookformax:
+            if p < (cur_max[1] - delta):
+                peaks.append((cur_max[0], cur_max[1], True))
+                cur_min = (n, p)
+                lookformax = False
+        else:
+            if p > (cur_min[1] + delta):
+                peaks.append((cur_min[0], cur_min[1], False))
+                cur_max = (n, p)
+                lookformax = True
+    return peaks

nilmtools/median.py

@@ -0,0 +1,43 @@
+#!/usr/bin/python
+import nilmtools.filter, scipy.signal
+
+def main(argv = None):
+    f = nilmtools.filter.Filter()
+    parser = f.setup_parser("Median Filter")
+    group = parser.add_argument_group("Median filter options")
+    group.add_argument("-z", "--size", action="store", type=int, default=25,
+                       help = "median filter size (default %(default)s)")
+    group.add_argument("-d", "--difference", action="store_true",
+                       help = "store difference rather than filtered values")
+
+    try:
+        args = f.parse_args(argv)
+    except nilmtools.filter.MissingDestination as e:
+        print "Source is %s (%s)" % (e.src.path, e.src.layout)
+        print "Destination %s doesn't exist" % (e.dest.path)
+        print "You could make it with a command like:"
+        print "  nilmtool -u %s create %s %s" % (e.dest.url,
+                                                 e.dest.path, e.src.layout)
+        raise SystemExit(1)
+
+    meta = f.client_src.stream_get_metadata(f.src.path)
+    f.check_dest_metadata({ "median_filter_source": f.src.path,
+                            "median_filter_size": args.size,
+                            "median_filter_difference": repr(args.difference) })
+
+    f.process_numpy(median_filter, args = (args.size, args.difference))
+
+def median_filter(data, interval, args, insert, final):
+    (size, diff) = args
+    (rows, cols) = data.shape
+    for i in range(cols - 1):
+        filtered = scipy.signal.medfilt(data[:, i+1], size)
+        if diff:
+            data[:, i+1] -= filtered
+        else:
+            data[:, i+1] = filtered
+    insert(data)
+    return rows
+
+if __name__ == "__main__":
+    main()

nilmtools/pipewatch.py

@@ -0,0 +1,176 @@
+#!/usr/bin/python
+
+import nilmdb.client
+from nilmdb.utils.printf import *
+import nilmdb.utils.lock
+import nilmtools
+
+import time
+import sys
+import os
+import argparse
+import subprocess
+import tempfile
+import threading
+import select
+import signal
+import Queue
+import daemon
+
+def parse_args(argv = None):
+    parser = argparse.ArgumentParser(
+        formatter_class = argparse.ArgumentDefaultsHelpFormatter,
+        version = nilmtools.__version__,
+        description = """\
+    Pipe data from 'generator' to 'consumer'.  This is intended to be
+    executed frequently from cron, and will exit if another copy is
+    already running.  If 'generator' or 'consumer' returns an error,
+    or if 'generator' stops sending data for a while, it will exit.
+
+    Intended for use with ethstream (generator) and nilm-insert
+    (consumer).  Commands are executed through the shell.
+    """)
+    parser.add_argument("-d", "--daemon", action="store_true",
+                        help="Run in background")
+    parser.add_argument("-l", "--lock", metavar="FILENAME", action="store",
+                        default=tempfile.gettempdir() +
+                        "/nilm-pipewatch.lock",
+                        help="Lock file for detecting running instance")
+    parser.add_argument("-t", "--timeout", metavar="SECONDS", action="store",
+                        type=float, default=30,
+                        help="Restart if no output from " +
+                        "generator for this long")
+    group = parser.add_argument_group("commands to execute")
+    group.add_argument("generator", action="store",
+                       help="Data generator (e.g. \"ethstream -r 8000\")")
+    group.add_argument("consumer", action="store",
+                       help="Data consumer (e.g. \"nilm-insert /foo/bar\")")
+    args = parser.parse_args(argv)
+
+    return args
+
+def reader_thread(queue, fd):
+    # Read from a file descriptor, write to queue.
+    try:
+        while True:
+            (r, w, x) = select.select([fd], [], [fd], 0.25)
+            if x:
+                raise Exception # generator died?
+            if not r:
+                # short timeout -- just try again.  This is to catch the
+                # fd being closed elsewhere, which is only detected
+                # when select restarts.
+                continue
+            data = os.read(fd, 65536)
+            if data == "": # generator EOF
+                raise Exception
+            queue.put(data)
+    except Exception:
+        queue.put(None)
+
+def watcher_thread(queue, procs):
+    # Put None in the queue if either process dies
+    while True:
+        for p in procs:
+            if p.poll() is not None:
+                queue.put(None)
+                return
+        time.sleep(0.25)
+
+def pipewatch(args):
+    # Run the processes, etc
+    with open(os.devnull, "r") as devnull:
+        generator = subprocess.Popen(args.generator, shell = True,
+                                     bufsize = -1, close_fds = True,
+                                     stdin = devnull,
+                                     stdout = subprocess.PIPE,
+                                     stderr = None,
+                                     preexec_fn = os.setpgrp)
+        consumer = subprocess.Popen(args.consumer, shell = True,
+                                    bufsize = -11, close_fds = True,
+                                    stdin = subprocess.PIPE,
+                                    stdout = None,
+                                    stderr = None,
+                                    preexec_fn = os.setpgrp)
+
+        queue = Queue.Queue(maxsize = 4)
+        reader = threading.Thread(target = reader_thread,
+                                  args = (queue, generator.stdout.fileno()))
+        reader.start()
+        watcher = threading.Thread(target = watcher_thread,
+                                   args = (queue, [generator, consumer]))
+        watcher.start()
+        try:
+            while True:
+                try:
+                    data = queue.get(True, args.timeout)
+                    if data is None:
+                        break
+                    consumer.stdin.write(data)
+                except Queue.Empty:
+                    # Timeout: kill the generator
+                    fprintf(sys.stderr, "pipewatch: timeout\n")
+                    generator.terminate()
+                    break
+
+            generator.stdout.close()
+            consumer.stdin.close()
+        except IOError:
+            fprintf(sys.stderr, "pipewatch: I/O error\n")
+
+        def kill(proc):
+            # Wait for a process to end, or kill it
+            def poll_timeout(proc, timeout):
+                for x in range(1+int(timeout / 0.1)):
+                    if proc.poll() is not None:
+                        break
+                    time.sleep(0.1)
+                return proc.poll()
+            try:
+                if poll_timeout(proc, 0.5) is None:
+                    os.killpg(proc.pid, signal.SIGTERM)
+                    if poll_timeout(proc, 0.5) is None:
+                        os.killpg(proc.pid, signal.SIGKILL)
+            except OSError:
+                pass
+            return poll_timeout(proc, 0.5)
+
+        # Wait for them to die, or kill them
+        cret = kill(consumer)
+        gret = kill(generator)
+
+        # Consume all remaining data in the queue until the reader
+        # and watcher threads are done
+        while reader.is_alive() or watcher.is_alive():
+            queue.get(True, 0.1)
+
+        fprintf(sys.stderr, "pipewatch: generator returned %d, " +
+                "consumer returned %d\n", gret, cret)
+        if gret == 0 and cret == 0:
+            sys.exit(0)
+        sys.exit(1)
+
+def main(argv = None):
+    args = parse_args(argv)
+
+    lockfile = open(args.lock, "w")
+    if not nilmdb.utils.lock.exclusive_lock(lockfile):
+        printf("pipewatch process already running (according to %s)\n",
+               args.lock)
+        sys.exit(0)
+    try:
+        # Run as a daemon if requested, otherwise run directly.
+        if args.daemon:
+            with daemon.DaemonContext(files_preserve = [ lockfile ]):
+                pipewatch(args)
+        else:
+            pipewatch(args)
+    finally:
+        # Clean up lockfile
+        try:
+            os.unlink(args.lock)
+        except OSError:
+            pass
+
+if __name__ == "__main__":
+    main()

nilmtools/prep.py

@@ -0,0 +1,192 @@
+#!/usr/bin/python
+
+# Spectral envelope preprocessor.
+# Requires two streams as input: the original raw data, and sinefit data.
+
+from nilmdb.utils.printf import *
+from nilmdb.utils.time import timestamp_to_human
+import nilmtools.filter
+import nilmdb.client
+from numpy import *
+import scipy.fftpack
+import scipy.signal
+#from matplotlib import pyplot as p
+import bisect
+from nilmdb.utils.interval import Interval
+
+def main(argv = None):
+    # Set up argument parser
+    f = nilmtools.filter.Filter()
+    parser = f.setup_parser("Spectral Envelope Preprocessor", skip_paths = True)
+    group = parser.add_argument_group("Prep options")
+    group.add_argument("-c", "--column", action="store", type=int,
+                       help="Column number (first data column is 1)")
+    group.add_argument("-n", "--nharm", action="store", type=int, default=4,
+                       help="number of odd harmonics to compute (default 4)")
+    group.add_argument("-N", "--nshift", action="store", type=int, default=1,
+                       help="number of shifted FFTs per period (default 1)")
+    exc = group.add_mutually_exclusive_group()
+    exc.add_argument("-r", "--rotate", action="store", type=float,
+                     help="rotate FFT output by this many degrees (default 0)")
+    exc.add_argument("-R", "--rotate-rad", action="store", type=float,
+                     help="rotate FFT output by this many radians (default 0)")
+
+    group.add_argument("srcpath", action="store",
+                       help="Path of raw input, e.g. /foo/raw")
+    group.add_argument("sinepath", action="store",
+                       help="Path of sinefit input, e.g. /foo/sinefit")
+    group.add_argument("destpath", action="store",
+                       help="Path of prep output, e.g. /foo/prep")
+
+    # Parse arguments
+    try:
+        args = f.parse_args(argv)
+    except nilmtools.filter.MissingDestination as e:
+        rec = "float32_%d" % (e.parsed_args.nharm * 2)
+        print "Source is %s (%s)" % (e.src.path, e.src.layout)
+        print "Destination %s doesn't exist" % (e.dest.path)
+        print "You could make it with a command like:"
+        print "  nilmtool -u %s create %s %s" % (e.dest.url, e.dest.path, rec)
+        raise SystemExit(1)
+
+    if f.dest.layout_count != args.nharm * 2:
+        print "error: need", args.nharm*2, "columns in destination stream"
+        raise SystemExit(1)
+
+    # Check arguments
+    if args.column is None or args.column < 1:
+        parser.error("need a column number >= 1")
+
+    if args.nharm < 1 or args.nharm > 32:
+        parser.error("number of odd harmonics must be 1-32")
+
+    if args.nshift < 1:
+        parser.error("number of shifted FFTs must be >= 1")
+
+    if args.rotate is not None:
+        rotation = args.rotate * 2.0 * pi / 360.0
+    else:
+        rotation = args.rotate_rad or 0.0
+
+    # Check the sine fit stream
+    client_sinefit = nilmdb.client.Client(args.url)
+    sinefit = nilmtools.filter.get_stream_info(client_sinefit, args.sinepath)
+    if not sinefit:
+        raise Exception("sinefit data not found")
+    if sinefit.layout != "float32_3":
+        raise Exception("sinefit data type is " + sinefit.layout
+                        + "; expected float32_3")
+
+    # Check and set metadata in prep stream
+    f.check_dest_metadata({ "prep_raw_source": f.src.path,
+                            "prep_sinefit_source": sinefit.path,
+                            "prep_column": args.column,
+                            "prep_rotation": repr(rotation),
+                            "prep_nshift": args.nshift })
+
+    # Find the intersection of the usual set of intervals we'd filter,
+    # and the intervals actually present in sinefit data.  This is
+    # what we will process.
+    filter_int = f.intervals()
+    sinefit_int = ( Interval(start, end) for (start, end) in
+                    client_sinefit.stream_intervals(
+                        args.sinepath, start = f.start, end = f.end) )
+    intervals = nilmdb.utils.interval.intersection(filter_int, sinefit_int)
+
+    # Run the process (using the helper in the filter module)
+    f.process_numpy(process, args = (client_sinefit, sinefit.path, args.column,
+                                     args.nharm, rotation, args.nshift),
+                    intervals = intervals)
+
+
+def process(data, interval, args, insert_function, final):
+    (client, sinefit_path, column, nharm, rotation, nshift) = args
+    rows = data.shape[0]
+    data_timestamps = data[:,0]
+
+    if rows < 2:
+        return 0
+
+    last_inserted = [nilmdb.utils.time.min_timestamp]
+    def insert_if_nonoverlapping(data):
+        """Call insert_function to insert data, but only if this
+        data doesn't overlap with other data that we inserted."""
+        if data[0][0] <= last_inserted[0]:
+            return
+        last_inserted[0] = data[-1][0]
+        insert_function(data)
+
+    processed = 0
+    out = zeros((1, nharm * 2 + 1))
+    # Pull out sinefit data for the entire time range of this block
+    for sinefit_line in client.stream_extract(sinefit_path,
+                                              data[0, 0], data[rows-1, 0]):
+        def prep_period(t_min, t_max, rot):
+            """
+            Compute prep coefficients from time t_min to t_max, which
+            are the timestamps of the start and end of one period.
+            Results are rotated by an additional extra_rot before
+            being inserted into the database.  Returns the maximum
+            index processed, or None if the period couldn't be
+            processed.
+            """
+            # Find the indices of data that correspond to (t_min, t_max)
+            idx_min = bisect.bisect_left(data_timestamps, t_min)
+            idx_max = bisect.bisect_left(data_timestamps, t_max)
+            if idx_min >= idx_max or idx_max >= len(data_timestamps):
+                return None
+
+            # Perform FFT over those indices
+            N = idx_max - idx_min
+            d = data[idx_min:idx_max, column]
+            F = scipy.fftpack.fft(d) * 2.0 / N
+
+            # If we wanted more harmonics than the FFT gave us, pad with zeros
+            if N < (nharm * 2):
+                F = r_[F, zeros(nharm * 2 - N)]
+
+            # Fill output data.
+            out[0, 0] = round(t_min)
+            for k in range(nharm):
+                Fk = F[2 * k + 1] * e**(rot * 1j * (k+1))
+                out[0, 2 * k + 1] = -imag(Fk) # Pk
+                out[0, 2 * k + 2] = real(Fk)  # Qk
+
+            insert_if_nonoverlapping(out)
+            return idx_max
+
+        # Extract sinefit data to get zero crossing timestamps.
+        # t_min = beginning of period
+        # t_max = end of period
+        (t_min, f0, A, C) = [ float(x) for x in sinefit_line.split() ]
+        t_max = t_min + 1e6 / f0
+
+        # Compute prep over shifted windows of the period
+        # (nshift is typically 1)
+        for n in range(nshift):
+            # Compute timestamps and rotations for shifted window
+            time_shift = n * (t_max - t_min) / nshift
+            shifted_min = t_min + time_shift
+            shifted_max = t_max + time_shift
+            angle_shift = n * 2 * pi / nshift
+            shifted_rot = rotation - angle_shift
+
+            # Run prep computation
+            idx_max = prep_period(shifted_min, shifted_max, shifted_rot)
+            if not idx_max:
+                break
+            processed = idx_max
+
+    # If we processed no data but there's lots in here, pretend we
+    # processed half of it.
+    if processed == 0 and rows > 10000:
+        processed = rows / 2
+        printf("%s: warning: no periods found; skipping %d rows\n",
+               timestamp_to_human(data[0][0]), processed)
+    else:
+        printf("%s: processed %d of %d rows\n",
+               timestamp_to_human(data[0][0]), processed, rows)
+    return processed
+
+if __name__ == "__main__":
+    main()

nilmtools/sinefit.py

@@ -0,0 +1,194 @@
+#!/usr/bin/python
+
+# Sine wave fitting.
+from nilmdb.utils.printf import *
+import nilmtools.filter
+import nilmtools.math
+import nilmdb.client
+from nilmdb.utils.time import (timestamp_to_human,
+                               timestamp_to_seconds,
+                               seconds_to_timestamp)
+
+from numpy import *
+from scipy import *
+#import pylab as p
+import sys
+
+def main(argv = None):
+    f = nilmtools.filter.Filter()
+    parser = f.setup_parser("Sine wave fitting")
+    group = parser.add_argument_group("Sine fit options")
+    group.add_argument('-c', '--column', action='store', type=int,
+                       help='Column number (first data column is 1)')
+    group.add_argument('-f', '--frequency', action='store', type=float,
+                       default=60.0,
+                       help='Approximate frequency (default: %(default)s)')
+    group.add_argument('-m', '--min-freq', action='store', type=float,
+                       help='Minimum valid frequency '
+                       '(default: approximate frequency / 2))')
+    group.add_argument('-M', '--max-freq', action='store', type=float,
+                       help='Maximum valid frequency '
+                       '(default: approximate frequency * 2))')
+    group.add_argument('-a', '--min-amp', action='store', type=float,
+                       default=20.0,
+                       help='Minimum signal amplitude (default: %(default)s)')
+
+    # Parse arguments
+    try:
+        args = f.parse_args(argv)
+    except nilmtools.filter.MissingDestination as e:
+        rec = "float32_3"
+        print "Source is %s (%s)" % (e.src.path, e.src.layout)
+        print "Destination %s doesn't exist" % (e.dest.path)
+        print "You could make it with a command like:"
+        print "  nilmtool -u %s create %s %s" % (e.dest.url, e.dest.path, rec)
+        raise SystemExit(1)
+
+    if args.column is None or args.column < 1:
+        parser.error("need a column number >= 1")
+    if args.frequency < 0.1:
+        parser.error("frequency must be >= 0.1")
+    if args.min_freq is None:
+        args.min_freq = args.frequency / 2
+    if args.max_freq is None:
+        args.max_freq = args.frequency * 2
+    if (args.min_freq > args.max_freq or
+        args.min_freq > args.frequency or
+        args.max_freq < args.frequency):
+        parser.error("invalid min or max frequency")
+    if args.min_amp < 0:
+        parser.error("min amplitude must be >= 0")
+
+    f.check_dest_metadata({ "sinefit_source": f.src.path,
+                            "sinefit_column": args.column })
+    f.process_numpy(process, args = (args.column, args.frequency, args.min_amp,
+                                     args.min_freq, args.max_freq))
+
+class SuppressibleWarning(object):
+    def __init__(self, maxcount = 10, maxsuppress = 100):
+        self.maxcount = maxcount
+        self.maxsuppress = maxsuppress
+        self.count = 0
+        self.last_msg = ""
+
+    def _write(self, sec, msg):
+        if sec:
+            now = timestamp_to_human(seconds_to_timestamp(sec)) + ": "
+        else:
+            now = ""
+        sys.stderr.write(now + msg)
+
+    def warn(self, msg, seconds = None):
+        self.count += 1
+        if self.count <= self.maxcount:
+            self._write(seconds, msg)
+        if (self.count - self.maxcount) >= self.maxsuppress:
+            self.reset(seconds)
+
+    def reset(self, seconds = None):
+        if self.count > self.maxcount:
+            self._write(seconds, sprintf("(%d warnings suppressed)\n",
+                                         self.count - self.maxcount))
+        self.count = 0
+
+def process(data, interval, args, insert_function, final):
+    (column, f_expected, a_min, f_min, f_max) = args
+    rows = data.shape[0]
+
+    # Estimate sampling frequency from timestamps
+    ts_min = timestamp_to_seconds(data[0][0])
+    ts_max = timestamp_to_seconds(data[-1][0])
+    if ts_min >= ts_max:
+        return 0
+    fs = (rows-1) / (ts_max - ts_min)
+
+    # Pull out about 3.5 periods of data at once;
+    # we'll expect to match 3 zero crossings in each window
+    N = max(int(3.5 * fs / f_expected), 10)
+
+    # If we don't have enough data, don't bother processing it
+    if rows < N:
+        return 0
+
+    warn = SuppressibleWarning(3, 1000)
+
+    # Process overlapping windows
+    start = 0
+    num_zc = 0
+    last_inserted_timestamp = None
+    while start < (rows - N):
+        this = data[start:start+N, column]
+        t_min = timestamp_to_seconds(data[start, 0])
+        t_max = timestamp_to_seconds(data[start+N-1, 0])
+
+        # Do 4-parameter sine wave fit
+        (A, f0, phi, C) = nilmtools.math.sfit4(this, fs)
+
+        # Check bounds.  If frequency is too crazy, ignore this window
+        if f0 < f_min or f0 > f_max:
+            warn.warn(sprintf("frequency %s outside valid range %s - %s\n",
+                              str(f0), str(f_min), str(f_max)), t_min)
+            start += N
+            continue
+
+        # If amplitude is too low, results are probably just noise
+        if A < a_min:
+            warn.warn(sprintf("amplitude %s below minimum threshold %s\n",
+                              str(A), str(a_min)), t_min)
+            start += N
+            continue
+
+        #p.plot(arange(N), this)
+        #p.plot(arange(N), A * sin(f0/fs * 2 * pi * arange(N) + phi) + C, 'g')
+
+        # Period starts when the argument of sine is 0 degrees,
+        # so we're looking for sample number:
+        #     n = (0 - phi) / (f0/fs * 2 * pi)
+        zc_n = (0 - phi) / (f0 / fs * 2 * pi)
+        period_n = fs/f0
+
+        # Add periods to make N positive
+        while zc_n < 0:
+            zc_n += period_n
+
+        last_zc = None
+        # Mark the zero crossings until we're a half period away
+        # from the end of the window
+        while zc_n < (N - period_n/2):
+            #p.plot(zc_n, C, 'ro')
+            t = t_min + zc_n / fs
+            if (last_inserted_timestamp is None or
+                t > last_inserted_timestamp):
+                insert_function([[seconds_to_timestamp(t), f0, A, C]])
+                last_inserted_timestamp = t
+                warn.reset(t)
+            else:
+                warn.warn("timestamp overlap\n", t)
+            num_zc += 1
+            last_zc = zc_n
+            zc_n += period_n
+
+        # Advance the window one quarter period past the last marked
+        # zero crossing, or advance the window by half its size if we
+        # didn't mark any.
+        if last_zc is not None:
+            advance = min(last_zc + period_n/4, N)
+        else:
+            advance = N/2
+        #p.plot(advance, C, 'go')
+        #p.show()
+
+        start = int(round(start + advance))
+
+    # Return the number of rows we've processed
+    warn.reset(last_inserted_timestamp)
+    if last_inserted_timestamp:
+        now = timestamp_to_human(seconds_to_timestamp(
+            last_inserted_timestamp)) + ": "
+    else:
+        now = ""
+    printf("%sMarked %d zero-crossings in %d rows\n", now, num_zc, start)
+    return start
+
+if __name__ == "__main__":
+    main()

nilmtools/trainola.py

@@ -0,0 +1,317 @@
+#!/usr/bin/python
+
+from nilmdb.utils.printf import *
+import nilmdb.client
+import nilmtools.filter
+import nilmtools.math
+from nilmdb.utils.time import (timestamp_to_human,
+                               timestamp_to_seconds,
+                               seconds_to_timestamp)
+from nilmdb.utils import datetime_tz
+from nilmdb.utils.interval import Interval
+
+import numpy as np
+import scipy
+import scipy.signal
+from numpy.core.umath_tests import inner1d
+import nilmrun
+from collections import OrderedDict
+import sys
+import time
+import functools
+import collections
+
+class DataError(ValueError):
+    pass
+
+def build_column_mapping(colinfo, streaminfo):
+    """Given the 'columns' list from the JSON data, verify and
+    pull out a dictionary mapping for the column names/numbers."""
+    columns = OrderedDict()
+    for c in colinfo:
+        col_num = c['index'] + 1  # skip timestamp
+        if (c['name'] in columns.keys() or col_num in columns.values()):
+            raise DataError("duplicated columns")
+        if (c['index'] < 0 or c['index'] >= streaminfo.layout_count):
+            raise DataError("bad column number")
+        columns[c['name']] = col_num
+    if not len(columns):
+        raise DataError("no columns")
+    return columns
+
+class Exemplar(object):
+    def __init__(self, exinfo, min_rows = 10, max_rows = 100000):
+        """Given a dictionary entry from the 'exemplars' input JSON,
+        verify the stream, columns, etc.  Then, fetch all the data
+        into self.data."""
+
+        self.name = exinfo['name']
+        self.url = exinfo['url']
+        self.stream = exinfo['stream']
+        self.start = exinfo['start']
+        self.end = exinfo['end']
+        self.dest_column = exinfo['dest_column']
+
+        # Get stream info
+        self.client = nilmdb.client.numpyclient.NumpyClient(self.url)
+        self.info = nilmtools.filter.get_stream_info(self.client, self.stream)
+        if not self.info:
+            raise DataError(sprintf("exemplar stream '%s' does not exist " +
+                                    "on server '%s'", self.stream, self.url))
+
+        # Build up name => index mapping for the columns
+        self.columns = build_column_mapping(exinfo['columns'], self.info)
+
+        # Count points
+        self.count = self.client.stream_count(self.stream, self.start, self.end)
+
+        # Verify count
+        if self.count == 0:
+            raise DataError("No data in this exemplar!")
+        if self.count < min_rows:
+            raise DataError("Too few data points: " + str(self.count))
+        if self.count > max_rows:
+            raise DataError("Too many data points: " + str(self.count))
+
+        # Extract the data
+        datagen = self.client.stream_extract_numpy(self.stream,
+                                                   self.start, self.end,
+                                                   self.info.layout,
+                                                   maxrows = self.count)
+        self.data = list(datagen)[0]
+
+        # Extract just the columns that were specified in self.columns,
+        # skipping the timestamp.
+        extract_columns = [ value for (key, value) in self.columns.items() ]
+        self.data = self.data[:,extract_columns]
+
+        # Fix the column indices in e.columns, since we removed/reordered
+        # columns in self.data
+        for n, k in enumerate(self.columns):
+            self.columns[k] = n
+
+        # Subtract the means from each column
+        self.data = self.data - self.data.mean(axis=0)
+
+        # Get scale factors for each column by computing dot product
+        # of each column with itself.
+        self.scale = inner1d(self.data.T, self.data.T)
+
+        # Ensure a minimum (nonzero) scale and convert to list
+        self.scale = np.maximum(self.scale, [1e-9]).tolist()
+
+    def __str__(self):
+        return sprintf("\"%s\" %s [%s] %s rows",
+                       self.name, self.stream, ",".join(self.columns.keys()),
+                       self.count)
+
+def timestamp_to_short_human(timestamp):
+    dt = datetime_tz.datetime_tz.fromtimestamp(timestamp_to_seconds(timestamp))
+    return dt.strftime("%H:%M:%S")
+
+def trainola_matcher(data, interval, args, insert_func, final_chunk):
+    """Perform cross-correlation match"""
+    ( src_columns, dest_count, exemplars ) = args
+    nrows = data.shape[0]
+
+    # We want at least 10% more points than the widest exemplar.
+    widest = max([ x.count for x in exemplars ])
+    if (widest * 1.1) > nrows:
+        return 0
+
+    # This is how many points we'll consider valid in the
+    # cross-correlation.
+    valid = nrows + 1 - widest
+    matches = collections.defaultdict(list)
+
+    # Try matching against each of the exemplars
+    for e in exemplars:
+        corrs = []
+
+        # Compute cross-correlation for each column
+        for col_name in e.columns:
+            a = data[:, src_columns[col_name]]
+            b = e.data[:, e.columns[col_name]]
+            corr = scipy.signal.fftconvolve(a, np.flipud(b), 'valid')[0:valid]
+
+            # Scale by the norm of the exemplar
+            corr = corr / e.scale[e.columns[col_name]]
+            corrs.append(corr)
+
+        # Find the peaks using the column with the largest amplitude
+        biggest = e.scale.index(max(e.scale))
+        peaks = nilmtools.math.peak_detect(corrs[biggest], 0.1)
+
+        # To try to reduce false positives, discard peaks where
+        # there's a higher-magnitude peak (either min or max) within
+        # one exemplar width nearby.
+        good_peak_locations = []
+        for (i, (n, p, is_max)) in enumerate(peaks):
+            if not is_max:
+                continue
+            ok = True
+            # check up to 'e.count' rows before this one
+            j = i-1
+            while ok and j >= 0 and peaks[j][0] > (n - e.count):
+                if abs(peaks[j][1]) > abs(p):
+                    ok = False
+                j -= 1
+
+            # check up to 'e.count' rows after this one
+            j = i+1
+            while ok and j < len(peaks) and peaks[j][0] < (n + e.count):
+                if abs(peaks[j][1]) > abs(p):
+                    ok = False
+                j += 1
+
+            if ok:
+                good_peak_locations.append(n)
+
+        # Now look at all good peaks
+        for row in good_peak_locations:
+            # Correlation for each column must be close enough to 1.
+            for (corr, scale) in zip(corrs, e.scale):
+                # The accepted distance from 1 is based on the relative
+                # amplitude of the column.  Use a linear mapping:
+                # scale 1.0 -> distance 0.1
+                # scale 0.0 -> distance 1.0
+                distance = 1 - 0.9 * (scale / e.scale[biggest])
+                if abs(corr[row] - 1) > distance:
+                    # No match
+                    break
+            else:
+                # Successful match
+                matches[row].append(e)
+
+    # Insert matches into destination stream.
+    matched_rows = sorted(matches.keys())
+    out = np.zeros((len(matched_rows), dest_count + 1))
+
+    for n, row in enumerate(matched_rows):
+        # Fill timestamp
+        out[n][0] = data[row, 0]
+
+        # Mark matched exemplars
+        for exemplar in matches[row]:
+            out[n, exemplar.dest_column + 1] = 1.0
+
+    # Insert it
+    insert_func(out)
+
+    # Return how many rows we processed
+    valid = max(valid, 0)
+    printf("  [%s] matched %d exemplars in %d rows\n",
+           timestamp_to_short_human(data[0][0]), np.sum(out[:,1:]), valid)
+    return valid
+
+def trainola(conf):
+    print "Trainola", nilmtools.__version__
+
+    # Load main stream data
+    url = conf['url']
+    src_path = conf['stream']
+    dest_path = conf['dest_stream']
+    start = conf['start']
+    end = conf['end']
+
+    # Get info for the src and dest streams
+    src_client = nilmdb.client.numpyclient.NumpyClient(url)
+    src = nilmtools.filter.get_stream_info(src_client, src_path)
+    if not src:
+        raise DataError("source path '" + src_path + "' does not exist")
+    src_columns = build_column_mapping(conf['columns'], src)
+
+    dest_client = nilmdb.client.numpyclient.NumpyClient(url)
+    dest = nilmtools.filter.get_stream_info(dest_client, dest_path)
+    if not dest:
+        raise DataError("destination path '" + dest_path + "' does not exist")
+
+    printf("Source:\n")
+    printf("  %s [%s]\n", src.path, ",".join(src_columns.keys()))
+    printf("Destination:\n")
+    printf("  %s (%s columns)\n", dest.path, dest.layout_count)
+
+    # Pull in the exemplar data
+    exemplars = []
+    for n, exinfo in enumerate(conf['exemplars']):
+        printf("Loading exemplar %d:\n", n)
+        e = Exemplar(exinfo)
+        col = e.dest_column
+        if col < 0 or col >= dest.layout_count:
+            raise DataError(sprintf("bad destination column number %d\n" +
+                                    "dest stream only has 0 through %d",
+                                    col, dest.layout_count - 1))
+        printf("  %s, output column %d\n", str(e), col)
+        exemplars.append(e)
+    if len(exemplars) == 0:
+        raise DataError("missing exemplars")
+
+    # Verify that the exemplar columns are all represented in the main data
+    for n, ex in enumerate(exemplars):
+        for col in ex.columns:
+            if col not in src_columns:
+                raise DataError(sprintf("Exemplar %d column %s is not "
+                                        "available in source data", n, col))
+
+    # Figure out which intervals we should process
+    intervals = ( Interval(s, e) for (s, e) in
+                  src_client.stream_intervals(src_path,
+                                              diffpath = dest_path,
+                                              start = start, end = end) )
+    intervals = nilmdb.utils.interval.optimize(intervals)
+
+    # Do the processing
+    rows = 100000
+    extractor = functools.partial(src_client.stream_extract_numpy,
+                                  src.path, layout = src.layout, maxrows = rows)
+    inserter = functools.partial(dest_client.stream_insert_numpy_context,
+                                 dest.path)
+    start = time.time()
+    processed_time = 0
+    printf("Processing intervals:\n")
+    for interval in intervals:
+        printf("%s\n", interval.human_string())
+        nilmtools.filter.process_numpy_interval(
+            interval, extractor, inserter, rows * 3,
+            trainola_matcher, (src_columns, dest.layout_count, exemplars))
+        processed_time += (timestamp_to_seconds(interval.end) -
+                           timestamp_to_seconds(interval.start))
+    elapsed = max(time.time() - start, 1e-3)
+
+    printf("Done. Processed %.2f seconds per second.\n",
+           processed_time / elapsed)
+
+def main(argv = None):
+    import simplejson as json
+    import sys
+
+    if argv is None:
+        argv = sys.argv[1:]
+    if len(argv) != 1 or argv[0] == '-h' or argv[0] == '--help':
+        printf("usage: %s [-h] [-v] <json-config-dictionary>\n\n", sys.argv[0])
+        printf("  Where <json-config-dictionary> is a JSON-encoded " +
+               "dictionary string\n")
+        printf("  with exemplar and stream data.\n\n")
+        printf("  See extras/trainola-test-param*.js in the nilmtools " +
+               "repository\n")
+        printf("  for examples.\n")
+        if len(argv) != 1:
+            raise SystemExit(1)
+        raise SystemExit(0)
+
+    if argv[0] == '-v' or argv[0] == '--version':
+        printf("%s\n", nilmtools.__version__)
+        raise SystemExit(0)
+
+    try:
+        # Passed in a JSON string (e.g. on the command line)
+        conf = json.loads(argv[0])
+    except TypeError as e:
+        # Passed in the config dictionary (e.g. from NilmRun)
+        conf = argv[0]
+
+    return trainola(conf)
+
+if __name__ == "__main__":
+    main()
+

setup.py

@@ -61,14 +61,27 @@ setup(name='nilmtools',
       long_description = "NILM Database Tools",
       license = "Proprietary",
       author_email = 'jim@jtan.com',
-      install_requires = [ 'nilmdb >= 1.3.0',
+      install_requires = [ 'nilmdb >= 1.8.5',
+                           'numpy',
+                           'scipy',
+                           'python-daemon >= 1.5',
+                           #'matplotlib',
                            ],
       packages = [ 'nilmtools',
                    ],
       entry_points = {
           'console_scripts': [
               'nilm-decimate = nilmtools.decimate:main',
+              'nilm-decimate-auto = nilmtools.decimate_auto:main',
               'nilm-insert = nilmtools.insert:main',
+              'nilm-copy = nilmtools.copy_one:main',
+              'nilm-prep = nilmtools.prep:main',
+              'nilm-copy-wildcard = nilmtools.copy_wildcard:main',
+              'nilm-sinefit = nilmtools.sinefit:main',
+              'nilm-cleanup = nilmtools.cleanup:main',
+              'nilm-median = nilmtools.median:main',
+              'nilm-trainola = nilmtools.trainola:main',
+              'nilm-pipewatch = nilmtools.pipewatch:main',
               ],
           },
       zip_safe = False,