prep: only process intervals present in both raw & sinefit

If the max scale in the exemplar was a column we weren't using, it
would bail out when looking for that correlation later.  Change things
around so exemplars in RAM only keep around the columns we care about.

Makefile

@@ -8,22 +8,37 @@ else
 	@echo "Try 'make install'"
 endif
 
-test: test_cleanup
+test: test_pipewatch
+
+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 "$$(cat extras/trainola-test-param-2.js)"
+	-nilmtool -u http://bucket/nilmdb remove -s min -e max \
+		/sharon/prep-a-matches
+	nilmtools/trainola.py "$$(cat extras/trainola-test-param.js)"
+
 
 test_cleanup:
-	src/cleanup.py -e extras/cleanup.cfg
-	src/cleanup.py extras/cleanup.cfg
+	nilmtools/cleanup.py -e extras/cleanup.cfg
+	nilmtools/cleanup.py extras/cleanup.cfg
 
 test_insert:
-	@make install >/dev/null
-	src/insert.py --file --dry-run  /test/foo </dev/null
+	nilmtools/insert.py --file --dry-run  /test/foo </dev/null
 
 test_copy:
-	@make install >/dev/null
-	src/copy_wildcard.py -U "http://nilmdb.com/bucket/" -D /lees*
+	nilmtools/copy_wildcard.py -U "http://nilmdb.com/bucket/" -D /lees*
 
-test_prep:
-	@make install >/dev/null
+/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
@@ -31,8 +46,9 @@ test_prep:
 	nilmtool create /test/sinefit float32_3
 	nilmtool create /test/prep float32_8
 	nilmtool insert -s '@0' -t -r 8000 /test/raw /tmp/raw.dat
-	src/sinefit.py -c 1 /test/raw /test/sinefit
-	src/prep.py -c 2 /test/raw /test/sinefit /test/prep
+	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_decimate:
@@ -40,8 +56,8 @@ test_decimate:
 	-@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 src/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 src/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
+	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
@@ -63,4 +79,4 @@ 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 +6,9 @@ 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-matplotlib
+  sudo apt-get install python-numpy python-scipy python-daemon
 
-  nilmdb (1.5.0+)
+  nilmdb (1.8.5+)
 
 Install:
 

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 +1,8 @@
+[/sharon/prep-*]
+keep = 1y
+
+[/sharon/raw]
+keep = 2w
+
+[/sharon/sinefit]
+keep = 1y

extras/sample-cron-scripts/crontab

@@ -0,0 +1,9 @@
+# Install this by running "crontab crontab" (will replace existing crontab)
+
+# m h dom mon dow cmd
+
+# Run NilmDB processing every 5 minutes
+*/5 * * * * chronic /home/nilm/data/process.sh
+
+# Check the capture process every minute
+*/1 * * * * chronic /home/nilm/data/capture.sh

extras/sample-cron-scripts/process.sh

@@ -0,0 +1,28 @@
+#!/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
+
+# sinefit on phase A voltage
+nilm-sinefit -c 5 /sharon/raw /sharon/sinefit
+
+# 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
+
+# decimate raw and prep data
+nilm-decimate-auto /sharon/raw /sharon/prep*
+
+# 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.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/_version.py

@@ -181,7 +181,7 @@ def versions_from_parentdir(parentdir_prefix, versionfile_source, verbose=False)
 
 tag_prefix = "nilmtools-"
 parentdir_prefix = "nilmtools-"
-versionfile_source = "src/_version.py"
+versionfile_source = "nilmtools/_version.py"
 
 def get_versions(default={"version": "unknown", "full": ""}, verbose=False):
     variables = { "refnames": git_refnames, "full": git_full }

nilmtools/filter.py

@@ -19,6 +19,10 @@ 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):
@@ -65,6 +69,70 @@ def get_stream_info(client, path):
         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])
+
 class Filter(object):
 
     def __init__(self, parser_description = None):
@@ -134,63 +202,52 @@ class Filter(object):
         self._parser = parser
         return parser
 
-    def interval_string(self, interval):
-        return sprintf("[ %s -> %s ]",
-                       timestamp_to_human(interval.start),
-                       timestamp_to_human(interval.end))
-
-    def parse_args(self, argv = None):
-        args = self._parser.parse_args(argv)
-
-        if args.dest_url is None:
-            args.dest_url = args.url
-        if args.url != args.dest_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
 
-        self._client_src = Client(args.url)
-        self._client_dest = Client(args.dest_url)
+        self._client_src = Client(url)
+        self._client_dest = Client(dest_url)
 
-        if (not self.interhost) and (args.srcpath == args.destpath):
-            self._parser.error("source and destination path must be different")
+        if (not self.interhost) and (srcpath == destpath):
+            raise ArgumentError("source and destination path must be different")
 
-        # Open and print info about the streams
-        self.src = get_stream_info(self._client_src, args.srcpath)
+        # Open the streams
+        self.src = get_stream_info(self._client_src, srcpath)
         if not self.src:
-            self._parser.error("source path " + args.srcpath + " not found")
+            raise ArgumentError("source path " + srcpath + " not found")
 
-        self.dest = get_stream_info(self._client_dest, args.destpath)
+        self.dest = get_stream_info(self._client_dest, destpath)
         if not self.dest:
-            raise MissingDestination(args, self.src,
-                                     StreamInfo(args.dest_url, [args.destpath]))
+            raise MissingDestination(parsed_args, self.src,
+                                     StreamInfo(dest_url, [destpath]))
 
-        print "Source:", self.src.string(self.interhost)
-        print "  Dest:", self.dest.string(self.interhost)
+        self.start = start
+        self.end = end
 
-        if args.dry_run:
-            for interval in self.intervals():
-                print self.interval_string(interval)
-            raise SystemExit(0)
+        # 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
-
-        self.start = args.start
-        self.end = args.end
-
+        if args.dry_run:
+            for interval in self.intervals():
+                print interval.human_string()
+            raise SystemExit(0)
         return args
 
-    def _optimize_int(self, it):
-        """Join and yield adjacent intervals from the iterator 'it'"""
-        saved_int = None
-        for interval in it:
-            if saved_int is not None:
-                if saved_int.end == interval.start:
-                    interval.start = saved_int.start
-                else:
-                    yield saved_int
-            saved_int = interval
-        if saved_int is not None:
-            yield saved_int
-
     def intervals(self):
         """Generate all the intervals that this filter should process"""
         self._using_client = True
@@ -217,12 +274,13 @@ class Filter(object):
                               self.src.path, diffpath = self.dest.path,
                               start = self.start, end = self.end) )
         # Optimize intervals: join intervals that are adjacent
-        for interval in self._optimize_int(intervals):
+        for interval in nilmdb.utils.interval.optimize(intervals):
             yield interval
         self._using_client = False
 
     # Misc helpers
-    def arg_time(self, toparse):
+    @staticmethod
+    def arg_time(toparse):
         """Parse a time string argument"""
         try:
             return nilmdb.utils.time.parse_time(toparse)
@@ -258,14 +316,21 @@ class Filter(object):
         self._client_dest.stream_update_metadata(self.dest.path, data)
 
     # The main filter processing method.
-    def process_numpy(self, function, args = None, rows = 100000):
-        """For all intervals that exist in self.src but don't exist in
-        self.dest, 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.
+    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 as:
-           def function(data, interval, args, insert_func, final)
+        # def function(data, interval, args, insert_func, final)
 
         'data': array of data to process -- may be empty
 
@@ -289,56 +354,18 @@ class Filter(object):
         being inserted will be ended at the timestamp of the first
         unprocessed data point.
         """
-        if args is None:
-            args = []
         extractor = NumpyClient(self.src.url).stream_extract_numpy
         inserter = NumpyClient(self.dest.url).stream_insert_numpy_context
 
-        for interval in self.intervals():
-            print "Processing", self.interval_string(interval)
-            with inserter(self.dest.path,
-                          interval.start, interval.end) as insert_ctx:
-                insert_function = insert_ctx.insert
-                old_array = np.array([])
-                for new_array in extractor(self.src.path,
-                                           interval.start, interval.end,
+        extractor_func = functools.partial(extractor, self.src.path,
                                            layout = self.src.layout,
-                                           maxrows = rows):
-                    # 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
+                                           maxrows = rows)
+        inserter_func = functools.partial(inserter, self.dest.path)
 
-                    # Pass it to the process function
-                    processed = function(array, interval, args,
-                                         insert_function, False)
-
-                    # Send any pending data
-                    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 old_array.shape[0] > 3 * 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_function, 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])
+        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
@@ -347,7 +374,7 @@ def main(argv = None):
     parser = f.setup_parser()
     args = f.parse_args(argv)
     for i in f.intervals():
-        print "Generic filter: need to handle", f.interval_string(i)
+        print "Generic filter: need to handle", i.human_string()
 
 if __name__ == "__main__":
     main()

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 +1,168 @@
+#!/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)
+        consumer = subprocess.Popen(args.consumer, shell = True,
+                                    bufsize = -11, close_fds = True,
+                                    stdin = subprocess.PIPE,
+                                    stdout = None, stderr = None)
+
+        queue = Queue.Queue(maxsize = 32)
+        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:
+                    proc.terminate()
+                    if poll_timeout(proc, 0.5) is None:
+                        proc.kill()
+            except OSError:
+                pass
+            return poll_timeout(proc, 0.5)
+
+        # Wait for them to die, or kill them
+        gret = kill(generator)
+        cret = kill(consumer)
+
+        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

@@ -12,6 +12,7 @@ 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
@@ -82,9 +83,20 @@ def main(argv = None):
                             "prep_column": args.column,
                             "prep_rotation": repr(rotation) })
 
-    # Run the processing function on all data
+    # 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))
+                                     args.nharm, rotation, args.nshift),
+                    intervals = intervals)
+
 
 def process(data, interval, args, insert_function, final):
     (client, sinefit_path, column, nharm, rotation, nshift) = args

nilmtools/sinefit.py

@@ -1,13 +1,18 @@
 #!/usr/bin/python
 
-# Sine wave fitting.  This runs about 5x faster than realtime on raw data.
-
+# Sine wave fitting.
+from nilmdb.utils.printf import *
 import nilmtools.filter
 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 operator
+import sys
 
 def main(argv = None):
     f = nilmtools.filter.Filter()
@@ -59,12 +64,40 @@ def main(argv = None):
     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
-    fs = 1e6 * (rows-1) / (data[-1][0] - data[0][0])
+    fs = (rows-1) / (timestamp_to_seconds(data[-1][0]) -
+                     timestamp_to_seconds(data[0][0]))
 
     # Pull out about 3.5 periods of data at once;
     # we'll expect to match 3 zero crossings in each window
@@ -74,26 +107,31 @@ def process(data, interval, args, insert_function, final):
     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 = data[start, 0]/1e6
-        t_max = data[start+N-1, 0]/1e6
+        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) = sfit4(this, fs)
 
         # Check bounds.  If frequency is too crazy, ignore this window
         if f0 < f_min or f0 > f_max:
-            print "frequency", f0, "outside valid range", f_min, "-", 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:
-            print "amplitude", A, "below minimum threshold", a_min
+            warn.warn(sprintf("amplitude %s below minimum threshold %s\n",
+                              str(A), str(a_min)), t_min)
             start += N
             continue
 
@@ -116,7 +154,13 @@ def process(data, interval, args, insert_function, final):
         while zc_n < (N - period_n/2):
             #p.plot(zc_n, C, 'ro')
             t = t_min + zc_n / fs
-            insert_function([[t * 1e6, f0, A, C]])
+            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
@@ -134,7 +178,13 @@ def process(data, interval, args, insert_function, final):
         start = int(round(start + advance))
 
     # Return the number of rows we've processed
-    print "Marked", num_zc, "zero-crossings in", start, "rows"
+    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
 
 def sfit4(data, fs):

nilmtools/trainola.py

@@ -0,0 +1,304 @@
+#!/usr/bin/python
+
+from nilmdb.utils.printf import *
+import nilmdb.client
+import nilmtools.filter
+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 peak_detect(data, delta):
+    """Simple min/max peak detection algorithm, taken from my code
+    in the disagg.m from the 10-8-5 paper"""
+    mins = [];
+    maxs = [];
+    cur_min = (None, np.inf)
+    cur_max = (None, -np.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):
+                maxs.append(cur_max)
+                cur_min = (n, p)
+                lookformax = False
+        else:
+            if p > (cur_min[1] + delta):
+                mins.append(cur_min)
+                cur_max = (n, p)
+                lookformax = True
+    return (mins, maxs)
+
+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_minmax = peak_detect(corrs[biggest], 0.1)
+        peaks = [ p[0] for p in peaks_minmax[1] ]
+
+        # Now look at every peak
+        for row in peaks:
+            # 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:
+        raise DataError("need one argument, either a dictionary or JSON string")
+
+    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

@@ -30,7 +30,7 @@ except ImportError:
 # Versioneer manages version numbers from git tags.
 # https://github.com/warner/python-versioneer
 import versioneer
-versioneer.versionfile_source = 'src/_version.py'
+versioneer.versionfile_source = 'nilmtools/_version.py'
 versioneer.versionfile_build = 'nilmtools/_version.py'
 versioneer.tag_prefix = 'nilmtools-'
 versioneer.parentdir_prefix = 'nilmtools-'
@@ -61,14 +61,14 @@ setup(name='nilmtools',
       long_description = "NILM Database Tools",
       license = "Proprietary",
       author_email = 'jim@jtan.com',
-      install_requires = [ 'nilmdb >= 1.6.0',
+      install_requires = [ 'nilmdb >= 1.8.5',
                            'numpy',
                            'scipy',
-                           'matplotlib',
+                           'python-daemon >= 1.5',
+                           #'matplotlib',
                            ],
       packages = [ 'nilmtools',
                    ],
-      package_dir = { 'nilmtools': 'src' },
       entry_points = {
           'console_scripts': [
               'nilm-decimate = nilmtools.decimate:main',
@@ -79,6 +79,9 @@ setup(name='nilmtools',
               '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,