Fix recommended layout

This converts data into big Numpy arrays and lets the user-provided
function process as much as they'd like at a time.

.gitignore

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

Makefile

@@ -1,5 +1,33 @@
+#URL="http://bucket.mit.edu:8080/nilmdb"
+URL="http://localhost/nilmdb"
+
 all:
+ifeq ($(INSIDE_EMACS), t)
+	@make test
+else
 	@echo "Try 'make install'"
+endif
+
+test:
+	@make install >/dev/null
+	src/copy_wildcard.py -U "http://nilmdb.com/bucket/" -D /lees*
+
+test_prep:
+	@make install >/dev/null
+	src/prep.py -c 3 \
+		/lees-compressor/no-leak/raw \
+		/lees-compressor/no-leak/sinefit \
+		/lees-compressor/no-leak/prep \
+	-s '2013-02-19 18:00:00' \
+	-r 0
+
+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 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
 
 version:
 	python setup.py version

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-matplotlib
 
   nilmdb (1.3.1+)
 
 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".
+

nilmtools/filter.py

@@ -1,66 +0,0 @@
-#!/usr/bin/python
-
-import nilmdb.client
-from nilmdb.utils.printf import *
-from nilmdb.utils.time import parse_time, format_time
-
-import time
-import sys
-import re
-import argparse
-
-class Filter(object):
-
-    def __init__(self, description = "Filter data"):
-        self.args = None
-        self._client = None
-        self.parse_args(description)
-
-    def parse_args(self, description):
-        parser = argparse.ArgumentParser(
-            description = description,
-            formatter_class = argparse.RawDescriptionHelpFormatter)
-        parser.add_argument("-u", "--url", action="store",
-                            default="http://localhost:12380/",
-                            help="Server URL (default: %(default)s)")
-        parser.add_argument("srcpath", action="store",
-                            help="Path of source stream, e.g. /foo/bar")
-        parser.add_argument("destpath", action="store",
-                            help="Path of destination stream, e.g. /foo/bar")
-        self.args = parser.parse_args()
-
-        self._client = nilmdb.client.Client(args.url)
-
-        if args.srcpath == args.destpath:
-            raise Exception("source and destination path must be different")
-
-        # 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)
-
-        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])
-
-        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])
-
-    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
-
-def main():
-    # 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
-
-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 = 'nilmtools/_version.py'
+versioneer.versionfile_source = 'src/_version.py'
 versioneer.versionfile_build = 'nilmtools/_version.py'
 versioneer.tag_prefix = 'nilmtools-'
 versioneer.parentdir_prefix = 'nilmtools-'
@@ -61,14 +61,22 @@ setup(name='nilmtools',
       long_description = "NILM Database Tools",
       license = "Proprietary",
       author_email = 'jim@jtan.com',
-      install_requires = [ 'nilmdb >= 1.3.0',
+      install_requires = [ 'nilmdb >= 1.4.6',
+                           'numpy',
+                           'scipy',
+                           'matplotlib',
                            ],
       packages = [ 'nilmtools',
                    ],
+      package_dir = { 'nilmtools': 'src' },
       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-copy-wildcard = nilmtools.copy_wildcard:main',
+              'nilm-sinefit = nilmtools.sinefit:main',
               ],
           },
       zip_safe = False,

src/_version.py

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

src/copy_one.py

@@ -0,0 +1,40 @@
+#!/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
+import numpy as np
+import sys
+
+def main(argv = None):
+    f = nilmtools.filter.Filter()
+    parser = f.setup_parser("Copy a stream")
+
+    # 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
+    meta = f.client_src.stream_get_metadata(f.src.path)
+    f.check_dest_metadata(meta)
+
+    # Copy all rows of data as ASCII strings
+    extractor = nilmdb.client.Client(f.src.url).stream_extract
+    inserter = nilmdb.client.Client(f.dest.url).stream_insert_context
+    for i in f.intervals():
+        print "Processing", f.interval_string(i)
+        with inserter(f.dest.path, i.start, i.end) as insert_ctx:
+            for row in extractor(f.src.path, i.start, i.end):
+                insert_ctx.insert(row + "\n")
+
+if __name__ == "__main__":
+    main()

src/copy_wildcard.py

@@ -0,0 +1,70 @@
+#!/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("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.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()

src/decimate.py

@@ -0,0 +1,81 @@
+#!/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):
+        n = f.src.layout_count // 3
+        f.process_python(function = decimate_again, rows = args.factor,
+                         args = (n,))
+    else:
+        n = f.src.layout_count
+        f.process_python(function = decimate_first, rows = args.factor,
+                         args = (n,))
+
+def decimate_first(data, n):
+    """Decimate original data -- result has 3 times as many columns"""
+    # For this simple calculation, converting to a Numpy array
+    # and doing the math is slower than just doing it directly.
+    rows = iter(data)
+    r_sum = r_min = r_max = rows.next()
+    for row in rows:
+        r_sum = map(operator.add, r_sum, row)
+        r_min = map(min, r_min, row)
+        r_max = map(max, r_max, row)
+    r_mean = [ x / len(data) for x in r_sum ]
+    return [ [ r_mean[0] ] + r_mean[1:] + r_min[1:] + r_max[1:] ]
+
+def decimate_again(data, n):
+    """Decimate already-decimated data -- result has the same number
+    of columns"""
+    rows = iter(data)
+    r = rows.next()
+    r_sum = r[0:(n+1)]
+    r_min = r[(n+1):(2*n+1)]
+    r_max = r[(2*n+1):(3*n+1)]
+    for r in rows:
+        r_sum = map(operator.add, r_sum, r[0:(n+1)])
+        r_min = map(min, r_min, r[(n+1):(2*n+1)])
+        r_max = map(max, r_max, r[(2*n+1):(3*n+1)])
+    r_mean = [ x / len(data) for x in r_sum ]
+    return [ r_mean + r_min + r_max ]
+
+if __name__ == "__main__":
+    main()

src/decimate_auto.py

@@ -0,0 +1,76 @@
+#!/usr/bin/python
+
+import nilmtools.filter
+import nilmtools.decimate
+import nilmdb.client
+import argparse
+
+def main(argv = None):
+    parser = argparse.ArgumentParser(
+        formatter_class = argparse.RawDescriptionHelpFormatter,
+        version = "1.0",
+        description = """\
+    Automatically create multiple decimations from a single source
+    stream, continuing until the last decimated level contains fewer
+    than 500 points total.
+    """)
+    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("--force-metadata", action="store_true",
+                        default = False,
+                        help="Force metadata changes if the dest "
+                        "doesn't match")
+    parser.add_argument("path", action="store",
+                        help='Path of base stream')
+    args = parser.parse_args(argv)
+
+    # Pull out info about the base stream
+    client = nilmdb.client.Client(args.url)
+
+    info = nilmtools.filter.get_stream_info(client, args.path)
+    if not info:
+        raise Exception("path " + args.path + " not found")
+
+    meta = client.stream_get_metadata(args.path)
+    if "decimate_source" in meta:
+        print "Stream", args.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" % (args.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)
+
+if __name__ == "__main__":
+    main()

src/filter.py

@@ -0,0 +1,413 @@
+#!/usr/bin/python
+
+from __future__ import absolute_import
+
+import nilmdb.client
+from nilmdb.client import Client
+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
+
+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])
+
+class Filter(object):
+
+    def __init__(self):
+        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
+
+    @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(
+            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)")
+        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("--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")
+            group.add_argument("destpath", action="store",
+                               help="Path of destination stream, e.g. /foo/bar")
+        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:
+            self.interhost = True
+
+        self._client_src = Client(args.url)
+        self._client_dest = Client(args.dest_url)
+
+        if (not self.interhost) and (args.srcpath == args.destpath):
+            self._parser.error("source and destination path must be different")
+
+        # Open and print info about the streams
+        self.src = get_stream_info(self._client_src, args.srcpath)
+        if not self.src:
+            self._parser.error("source path " + args.srcpath + " not found")
+
+        self.dest = get_stream_info(self._client_dest, args.destpath)
+        if not self.dest:
+            raise MissingDestination(args, self.src,
+                                     StreamInfo(args.dest_url, [args.destpath]))
+
+        print "Source:", self.src.string(self.interhost)
+        print "  Dest:", self.dest.string(self.interhost)
+
+        if args.dry_run:
+            for interval in self.intervals():
+                print self.interval_string(interval)
+            raise SystemExit(0)
+
+        self.force_metadata = args.force_metadata
+
+        self.start = args.start
+        self.end = args.end
+
+        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
+
+        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 self._optimize_int(intervals):
+            yield interval
+        self._using_client = False
+
+    # Misc helpers
+    def arg_time(self, 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.  If
+        there's no conflict, update the metadata to match 'data'."""
+        metadata = self._client_dest.stream_get_metadata(self.dest.path)
+        if not self.force_metadata:
+            for key in data:
+                wanted = str(data[key])
+                val = metadata.get(key, wanted)
+                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)
+
+    # Main processing helper
+    def process_python(self, function, rows, args = None, partial = False):
+        """Process data in chunks of 'rows' data at a time.
+
+        This provides data as nested Python lists and expects the same
+        back.
+
+        function: function to process the data
+        rows: maximum number of rows to pass to 'function' at once
+        args: tuple containing extra arguments to pass to 'function'
+        partial: if true, less than 'rows' may be passed to 'function'.
+                 if false, partial data at the end of an interval will
+                 be dropped.
+
+        'function' should be defined like:
+            function(data, *args)
+        It will be passed a list containing up to 'rows' rows of
+        data from the source stream, and any arguments passed in
+        'args'.  It should transform the data as desired, and return a
+        new list of rdata, which will be inserted into the destination
+        stream.
+        """
+        if args is None:
+            args = []
+        extractor = Client(self.src.url).stream_extract
+        inserter = Client(self.dest.url).stream_insert_context
+
+        # Parse input data.  We use homogenous types for now, which
+        # means the timestamp type will be either float or int.
+        if "int" in self.src.layout_type:
+            parser = lambda line: [ int(x) for x in line.split() ]
+        else:
+            parser = lambda line: [ float(x) for x in line.split() ]
+
+        # Format output data.
+        formatter = lambda row: " ".join([repr(x) for x in row]) + "\n"
+
+        for interval in self.intervals():
+            print "Processing", self.interval_string(interval)
+            with inserter(self.dest.path,
+                          interval.start, interval.end) as insert_ctx:
+                src_array = []
+                for line in extractor(self.src.path,
+                                      interval.start, interval.end):
+                    # Read in data
+                    src_array.append([ float(x) for x in line.split() ])
+
+                    if len(src_array) == rows:
+                        # Pass through filter function
+                        dest_array = function(src_array, *args)
+
+                        # Write result to destination
+                        out = [ formatter(row) for row in dest_array ]
+                        insert_ctx.insert("".join(out))
+
+                        # Clear source array
+                        src_array = []
+
+                # Take care of partial chunk
+                if len(src_array) and partial:
+                    dest_array = function(src_array, *args)
+                    out = [ formatter(row) for row in dest_array ]
+                    insert_ctx.insert("".join(out))
+
+    # Like process_python, but provides Numpy arrays and allows for
+    # partial processing.
+    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.
+
+        'function' should be defined as:
+           def function(data, interval, args, insert_func, final)
+
+        '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 args is None:
+            args = []
+        extractor = Client(self.src.url).stream_extract
+        inserter = Client(self.dest.url).stream_insert_context
+
+        # Format output data.
+        formatter = lambda row: " ".join([repr(x) for x in row]) + "\n"
+
+        def batch(iterable, size):
+            c = itertools.count()
+            for k, g in itertools.groupby(iterable, lambda x: c.next() // size):
+                yield g
+
+        for interval in self.intervals():
+            print "Processing", self.interval_string(interval)
+            with inserter(self.dest.path,
+                          interval.start, interval.end) as insert_ctx:
+                def insert_function(array):
+                    s = cStringIO.StringIO()
+                    if len(np.shape(array)) != 2:
+                        raise Exception("array must be 2-dimensional")
+                    np.savetxt(s, array)
+                    insert_ctx.insert(s.getvalue())
+
+                extract = extractor(self.src.path, interval.start, interval.end)
+                old_array = np.array([])
+                for batched in batch(extract, rows):
+                    # Read in this batch of data
+                    new_array = np.loadtxt(batched)
+
+                    # 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 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:
+                    function(old_array, interval, args, insert_function, True)
+
+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()
+    parser = f.setup_parser()
+    args = f.parse_args(argv)
+    for i in f.intervals():
+        print "Generic filter: need to handle", f.interval_string(i)
+
+if __name__ == "__main__":
+    main()

src/insert.py

@@ -2,8 +2,11 @@
 
 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
@@ -15,8 +18,11 @@ class ParseError(Exception):
         msg = filename + ": " + error
         super(ParseError, self).__init__(msg)
 
-def parse_args():
-    parser = argparse.ArgumentParser(description = """\
+def parse_args(argv = None):
+    parser = argparse.ArgumentParser(
+        formatter_class = argparse.RawDescriptionHelpFormatter,
+        version = nilmtools.__version__,
+        description = """\
     Insert data from ethstream, either live (using the system time as a
     reference) or prerecorded (using comments in the file as a reference).
 
@@ -24,28 +30,29 @@ def parse_args():
     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)
+    """)
     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,
+    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",
                         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()
+                        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))
 
     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)
 
@@ -55,20 +62,22 @@ def main(args = None):
     # 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
 
     # clock_ts is the imprecise "real" timestamp (from the filename,
     # comments, or or system clock)
     clock_ts = None
 
     def print_clock_updated():
-        printf("Clock time updated to %s\n", format_time(clock_ts))
+        printf("Clock time updated to %s\n", timestamp_to_human(clock_ts))
         if data_ts_base != 0:
             diff = 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))
 
     with client.stream_insert_context(args.path) as stream:
         for f in args.infile:
@@ -86,7 +95,7 @@ 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) - seconds_to_timestamp(3600)
                 print_clock_updated()
             except ValueError:
                 pass
@@ -95,7 +104,8 @@ def main(args = None):
 
             # Read each line
             for line in f:
-                data_ts = data_ts_base + data_ts_inc * data_ts_step
+                data_ts = data_ts_base + rate_to_period(data_ts_rate,
+                                                        data_ts_inc)
 
                 # If no content other than the newline, skip it
                 if len(line) <= 1:
@@ -104,7 +114,7 @@ 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:])
                         print_clock_updated()
                     except ValueError:
                         pass
@@ -112,30 +122,30 @@ def main(args = None):
 
                 # If inserting live, use clock timestamp
                 if live:
-                    clock_ts = time.time()
+                    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 - seconds_to_timestamp(10)) > 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))
                         raise ParseError(filename, err)
 
-                    if (data_ts + 10) < clock_ts:
+                    if (data_ts + seconds_to_timestamp(10)) < 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
@@ -160,7 +170,7 @@ def main(args = None):
                     continue
 
                 # Insert it
-                stream.insert("%.6f %s" % (data_ts, line))
+                stream.insert("%d %s" % (data_ts, line))
     print "Done"
 
 if __name__ == "__main__":

src/prep.py

@@ -0,0 +1,126 @@
+#!/usr/bin/python
+
+# Spectral envelope preprocessor.
+# Requires two streams as input: the original raw data, and sinefit data.
+
+import nilmtools.filter
+import nilmdb.client
+from numpy import *
+import scipy.fftpack
+import scipy.signal
+from matplotlib import pyplot as p
+import bisect
+
+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")
+    exc = group.add_mutually_exclusive_group()
+    exc.add_argument("-r", "--rotate", action="store", type=float,
+                     help="rotate FFT output by this many degrees")
+    exc.add_argument("-R", "--rotate-rad", action="store", type=float,
+                     help="rotate FFT output by this many radians")
+
+    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)
+
+    # 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.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 })
+
+    # Run the processing function on all data
+    f.process_numpy(process, args = (client_sinefit, sinefit.path, args.column,
+                                     args.nharm, rotation))
+
+def process(data, interval, args, insert_function, final):
+    (client, sinefit_path, column, nharm, rotation) = args
+    rows = data.shape[0]
+    data_timestamps = data[:,0]
+
+    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]):
+        # Extract sinefit data to get zero crossing timestamps
+        (t_min, f0, A, C) = [ float(x) for x in sinefit_line.split() ]
+        t_max = t_min + 1e6 / f0
+
+        # 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:
+            # something's wonky; ignore this period
+            continue
+        if idx_max >= len(data_timestamps):
+            # max is likely past the end of our chunk, so stop
+            # processing this chunk now.
+            break
+
+        # Perform FFT over those indices
+        N = idx_max - idx_min
+        d = data[idx_min:idx_max, column]
+        F = scipy.fftpack.fft(d) / N
+
+        # If we wanted more harmonics than we have, pad with zeros
+        if N < (nharm * 2):
+            F = r_[F, zeros(nharm * 2 - N)]
+
+        # Fill output data
+        out[0, 0] = t_min
+        for k in range(nharm):
+            Fk = F[2 * k + 1] * e**(rotation * 1j * k)
+            out[0, 2 * k + 1] = -imag(Fk) # Pk
+            out[0, 2 * k + 2] = real(Fk)  # Qk
+
+        # Insert it and continue
+        insert_function(out)
+        processed = idx_max
+
+    print "Processed", processed, "of", rows, "rows"
+    return processed
+
+if __name__ == "__main__":
+    main()

src/sinefit.py

@@ -0,0 +1,187 @@
+#!/usr/bin/python
+
+# Sine wave fitting.  This runs about 5x faster than realtime on raw data.
+
+import nilmtools.filter
+import nilmdb.client
+from numpy import *
+from scipy import *
+#import pylab as p
+import operator
+
+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)')
+
+    # 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")
+
+    f.check_dest_metadata({ "sinefit_source": f.src.path,
+                            "sinefit_column": args.column })
+    f.process_numpy(process, args = (args.column, args.frequency))
+
+def process(data, interval, args, insert_function, final):
+    (column, f_expected) = args
+    rows = data.shape[0]
+
+    # Estimate sampling frequency from timestamps
+    fs = 1e6 * (rows-1) / (data[-1][0] - data[0][0])
+
+    # 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
+
+    # Process overlapping windows
+    start = 0
+    num_zc = 0
+    while start < (rows - N):
+        this = data[start:start+N, column]
+        t_min = data[start, 0]/1e6
+        t_max = data[start+N-1, 0]/1e6
+
+        # 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_expected/2) or f0 > (f_expected*2):
+            print "frequency", f0, "too far from expected value", f_expected
+            start += N
+            continue
+
+        #p.plot(arange(N), this)
+        #p.plot(arange(N), A * cos(f0/fs * 2 * pi * arange(N) + phi) + C, 'g')
+
+        # Period starts when the argument of cosine is 3*pi/2 degrees,
+        # so we're looking for sample number:
+        #     n = (3 * pi / 2 - phi) / (f0/fs * 2 * pi)
+        zc_n = (3 * pi / 2 - 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
+            insert_function([[t * 1e6, f0, A, C]])
+            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
+    print "Marked", num_zc, "zero-crossings in", start, "rows"
+    return start
+
+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 * cos(f0/fs * 2 * pi * n + phi) + C
+      where n is sample number.  Or, as a function of time:
+        x(t) = A * cos(f0 * 2 * pi * t + phi) + C
+
+    by Jim Paris
+    (Verified to match sfit4.m)
+    """
+    N = len(data)
+    t = linspace(0, (N-1) / 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])
+    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
+
+    # Convert to Hz
+    f0 = i * fs / N
+
+    ## Fit it
+    # first guess for A0, B0 using 3-parameter fit (step c)
+    w = 2*pi*f0
+    D = c_[cos(w*t), sin(w*t), ones(N)]
+    s = linalg.lstsq(D, data)[0]
+
+    # Now iterate 6 times (step i)
+    for idx in range(6):
+        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)
+    try:
+        phi = -arctan2(s[1], s[0]) # eqn B.22
+    except TypeError:
+        # something broke down, just return zeros
+        return (0, 0, 0, 0)
+    C = s[2]
+
+    return (A, f0, phi, C)
+
+if __name__ == "__main__":
+    main()