def initialize(self):
"""
tables.EArray(parentnode, name, atom=None, shape=None,
title='', filters=None, expectedrows=None,
chunkshape=None, byteorder=None, _log=True)[source]
"""
self.m.log(1, '+++Init method of MCWaveform algorithm+++')
self.NPMTS = int(12)
self.LEN_PMT = int(599999)
self.NSIPM = int(1792)
self.LEN_SIPM = int(600)
path = "/Users/jjgomezcadenas/Documents/Development/NEXT/data/Waveforms/"
file = "WF_Tl_0.h5"
self.NEVENTS = self.logman["CNTJob"].ints["NEVENTS"]
self.h5f = tables.open_file(path + file,
"w",
filters=tables.Filters(complib="blosc",
complevel=9))
self.pmtrd = self.h5f.create_earray(self.h5f.root,
"pmtrd",
atom=tables.IntAtom(),
shape=(0, self.NPMTS,
self.LEN_PMT),
expectedrows=self.NEVENTS)
self.sipmrd = self.h5f.create_earray(self.h5f.root,
"sipmrd",
atom=tables.IntAtom(),
shape=(0, self.NSIPM,
self.LEN_SIPM),
expectedrows=self.NEVENTS)
group = self.h5f.create_group(self.h5f.root, "Detector")
self.geom_table = self.h5f.create_table(group, "DetectorGeometry",
DetectorGeometry,
"DetectorGeometry",
tables.Filters(0))
group = self.h5f.create_group(self.h5f.root, "Sensors")
self.pmt_table = self.h5f.create_table(group, "DataPMT", DataPMT,
"DataPMT", tables.Filters(0))
self.sipm_table = self.h5f.create_table(group, "DataSiPM", DataSiPM,
"DataSiPM", tables.Filters(0))
group = self.h5f.create_group(self.h5f.root, "MC")
self.MCTrack_table = self.h5f.create_table(group, "MCTracks",
MCTrack, "MCTracks",
tables.Filters(0))
# self.h5f = tables.open_file("pmtrd.h5", "a",
# filters=tables.Filters(complib="blosc", complevel=9))
#self.pmt = self.h5f.create_table(self.h5f.root, "pmt", PMTRD)
self.t = time()
self.n_evt = 0
return
def init_output(outfile):
"""
Creates a timestamped output directory and writes header to output file.
"""
with tables.open_file(outfile, 'w') as f:
## Create extendable arrays so we can incrementally write output
f.create_earray(f.root, 'ancs', atom=tables.IntAtom(), shape=(0, ))
f.create_earray(f.root, 'liks', atom=tables.FloatAtom(), shape=(0, ))
## Trees, which are variable-length, must be added individually
f.create_vlarray(f.root, 'trees', atom=tables.IntAtom())
f.create_vlarray(f.root, 'genotypes', atom=tables.IntAtom())
def populate(f, nlevels):
g = f.root
#arr = numpy.zeros((10,), "f4")
#descr = {'f0': tables.Int32Col(), 'f1': tables.Float32Col()}
for i in range(nlevels):
#dset = f.create_array(g, "DS1", arr)
#dset = f.create_array(g, "DS2", arr)
f.create_carray(g, "DS1", tb.IntAtom(), (10,))
f.create_carray(g, "DS2", tb.IntAtom(), (10,))
#dset = f.create_table(g, "DS1", descr)
#dset = f.create_table(g, "DS2", descr)
f.create_group(g, 'group2_')
g = f.create_group(g, 'group')
def open_or_create_dataset_file(filename, filters, groups, add_classes): if os.path.exists(filename): return tables.open_file(filename, mode='r+') file = tables.open_file(filename, mode='w') for i in groups: file.create_group(file.root, i) file.create_carray(file.root, 'count', atom=tables.IntAtom(), shape=(1,), filters=filters) if add_classes: file.create_earray(file.root, 'classes', atom=tables.StringAtom(25), shape=(0,), filters=filters) file.create_earray(file.root, 'train', atom=tables.IntAtom(), shape=(0,), filters=filters) file.create_earray(file.root, 'test', atom=tables.IntAtom(), shape=(0,), filters=filters) file.root.count[0] = 0 return file
def populate(f, nlevels):
g = f.root
arr = numpy.zeros((10, ), "f4")
recarr = numpy.zeros((10, ), "i4,f4")
descr = {'f0': tables.Int32Col(), 'f1': tables.Float32Col()}
for i in range(nlevels):
#dset = f.createArray(g, "DS1", arr)
#dset = f.createArray(g, "DS2", arr)
dset = f.createCArray(g, "DS1", tables.IntAtom(), (10, ))
dset = f.createCArray(g, "DS2", tables.IntAtom(), (10, ))
#dset = f.createTable(g, "DS1", descr)
#dset = f.createTable(g, "DS2", descr)
group2 = f.createGroup(g, 'group2_')
g = f.createGroup(g, 'group')
def __init__(self, database: AbstractDB):
"""
Initialize the atoms for meta-data (types, valid tag, and splits)
Args:
database (AbstractDB): Associated Database object
"""
super().__init__(database)
self.filename_atom = tables.StringAtom(itemsize=255)
self.types_atom = tables.StringAtom(itemsize=255)
# whether the patch is valid.
self.valid_atom = tables.BoolAtom(shape=(), dflt=False)
# save the meta info: split
# noinspection PyArgumentList
self.file_list_atom = tables.StringAtom(itemsize=get_path_limit())
# noinspection PyArgumentList
self.split_atom = tables.IntAtom(shape=(), dflt=False)
self.hdf5_organizer = H5Organizer(self.database,
self.database.group_level)
self.data_extractor = DataExtractor(self.database)
self.weight_writer = WeightCollector(
self.database,
self.data_extractor,
weight_counter=self.database.weight_counter_callable)
self.data_size = {}
def test99b_nonScalarEnum(self):
"""Describing an enumerated column of non-scalars (not implemented)."""
colors = {'red': (1, 2, 3)}
self.assertRaises(NotImplementedError,
self._createCol,
colors,
'red',
base=tables.IntAtom(shape=3))
def write_carray(file, nchildren, niter):
for i in range(niter):
fileh = tables.openFile(file, mode="w")
for child in range(nchildren):
fileh.createCArray(fileh.root, 'array' + str(child),
tables.IntAtom(), (2, ), "child: %d" % child)
show_mem("After creating. Iter %s" % i)
fileh.close()
show_mem("After close")
def write_vlarray(file, nchildren, niter):
for i in range(niter):
fileh = tables.openFile(file, mode="w")
for child in range(nchildren):
vl = fileh.createVLArray(fileh.root, 'array' + str(child),
tables.IntAtom(), "child: %d" % child)
vl.append([1, 2, 3])
show_mem("After creating. Iter %s" % i)
fileh.close()
show_mem("After close")
def write_earray(file, nchildren, niter):
for i in range(niter):
fileh = tables.open_file(file, mode="w")
for child in range(nchildren):
ea = fileh.create_earray(fileh.root, 'array' + str(child),
tables.IntAtom(), shape=(0,),
title="child: %d" % child)
ea.append([1, 2, 3])
show_mem("After creating. Iter %s" % i)
fileh.close()
show_mem("After close")
def create_db(filename, params, total_env_count=None, traj_per_env=None):
"""
:param filename: file name for database
:param params: dotdict describing the domain
:param total_env_count: total number of environments in the dataset (helps to preallocate space)
:param traj_per_env: number of trajectories per environment
"""
N = params.grid_n
M = params.grid_m
num_state = N * M
if total_env_count is not None and traj_per_env is not None:
total_traj_count = total_env_count * traj_per_env
else:
total_traj_count = 0
if os.path.isfile(filename):
print (filename + " already exitst, opening.")
return tables.open_file(filename, mode='a')
db = tables.open_file(filename, mode='w')
db.create_earray(db.root, 'envs', tables.IntAtom(), shape=(0, N, M), expectedrows=total_env_count)
db.create_earray(db.root, 'expRs', tables.FloatAtom(), shape=(0, ), expectedrows=total_traj_count)
db.create_earray(db.root, 'valids', tables.IntAtom(), shape=(0, ), expectedrows=total_traj_count)
db.create_earray(db.root, 'bs', tables.FloatAtom(), shape=(0, num_state), expectedrows=total_traj_count)
db.create_earray(db.root, 'steps', tables.IntAtom(),
shape=(0, 3), # state, action, observation
expectedrows=total_traj_count * 10) # rough estimate
db.create_earray(db.root, 'samples', tables.IntAtom(),
shape=(0, 6), # env_id, goal_state, step_id, traj_length, collisions, failed
expectedrows=total_traj_count)
db.create_earray(db.root, 'qmdpBeliefs', tables.FloatAtom(), shape=(0, num_state,),expectedrows=total_traj_count*10)
return db
def init_h5_result_file(h5, expectedrows=50000):
"""
Receives a h5 file that has just been created,
creates the proper arrays:
- query
- target
- position
- n_results
"""
group = h5.createGroup("/",'results','general, sole group')
h5.createEArray(group,'query',tables.StringAtom(18,shape=()),(0,),
'tid of the query',
expectedrows=expectedrows)
h5.createEArray(group,'target',tables.StringAtom(18,shape=()),(0,),
'tid of the target',
expectedrows=expectedrows)
h5.createEArray(group,'pos',tables.IntAtom(shape=()),(0,),
'position of the target in the result list',
expectedrows=expectedrows)
h5.createEArray(group,'n_results',tables.IntAtom(shape=()),(0,),
'lenght of the result list returned by query',
expectedrows=expectedrows)
# done
return
def test19_getCutNodes(self):
"""Check the getCutNodes method.
"""
# Add a couple of nodes to the hidden group
tmp_db = VTAPP.dbManager.getDB(
VTAPP.dbManager.tmp_filepath).getH5File()
tmp_db.createGroup('/_p_cutNode', 'Group_A')
tmp_db.createCArray('/_p_cutNode', 'Hidden_CArray', tables.IntAtom(),
(3, 3))
tmp_db.flush()
cut_nodes = VTAPP.dbManager.getCutNodes()
cut_nodes.sort()
expected = ['Group_A', 'Hidden_CArray']
self.assertEqual(cut_nodes, expected,
'The retrieved list of cut nodes is wrong')
def combine_partial_contribs(partial_files, outfile):
"""
Combines the sparse results of several allele dropping simulations
into a single sparse array.
"""
## Dict of sparse contribs per region
region_contribs = defaultdict(initialize_sparse_array)
for pf in partial_files:
print "Loading contribs from", pf
with tables.open_file(pf, 'r') as f:
## Iterate through each region node in the sparse file
for partial_node in f.list_nodes(f.root.sparse_hist):
## Load sparse data
region = partial_node.name
r, c, d = np.transpose(partial_node[:])
## Add results to total
new_tot = append_sparse(region_contribs[region], r, c, d)
region_contribs[region] = new_tot
## Write results to file
with tables.open_file(outfile, 'w') as f:
filters = tables.Filters(complevel=5, complib='blosc')
g = f.create_group(f.root, 'sparse_hist')
for region, contribs in region_contribs.iteritems():
print "Writing contribs for region:", region
## Transpose data so max row size is not exceeded
r, c, d = contribs.row, contribs.col, contribs.data
contribs_array = np.transpose(np.vstack([r, c, d]))
## Store in compressed array
ca = f.create_carray(g,
region.strip(),
tables.IntAtom(),
shape=(contribs_array.shape),
filters=filters)
ca[:] = contribs_array
## Store number of inds in region
with tables.open_file(partial_files[0], 'r') as pf:
raw_node = pf.get_node(pf.root.raw, str(region))
ninds_region = raw_node._v_attrs['ninds']
f.set_node_attr(ca, 'ninds', ninds_region)
def create_hdf_arrays(file_name, ports, dig_in, emg_port, emg_channels):
hf5 = tables.open_file(file_name, 'r+')
n_electrodes = len(ports) * 32
atom = tables.IntAtom()
# Create arrays for digital inputs
for i in dig_in:
dig_inputs = hf5.create_earray('/digital_in', 'dig_in_%i' % i, atom,
(0, ))
# Create arrays for neural electrodes, and make directories to store stuff coming out from blech_process
for i in range(n_electrodes - len(emg_channels)):
el = hf5.create_earray('/raw', 'electrode%i' % i, atom, (0, ))
# Create arrays for EMG electrodes
for i in range(len(emg_channels)):
el = hf5.create_earray('/raw_emg', 'emg%i' % i, atom, (0, ))
# Close the hdf5 file
hf5.close()
def execute(self, context):
scene = context.scene
trkr = bpy.data.objects['tracker1'] # this script looks for an object named tracker1
fp = scene.render.filepath # get existing output path
handler = lose.Loser(os.path.normpath(f'{fp}/ground_truth.h5'))
handler.new_group(fmode='w', mat44=(4, 4), pos=(3,), rot_q=(4,))
handler.new_group(atom=t.IntAtom(), frame_id=(1,))
print ('starting to gather data\n\nframes will be saved to "' + os.path.normpath(f'{fp}/frames/') + '"')
print ('this handler will be used to save data:')
print (handler)
print ('starting render...\n')
scene.render.filepath = fp
try:
with handler:
# sequence length is pulled from blender animation duration settings
for i in range(scene.frame_start, scene.frame_end+1, scene.frame_step):
scene.frame_set(i)
scene.render.filepath = os.path.normpath(f'{fp}/frames/{i}')
bpy.ops.wm.redraw_timer(type='DRAW_WIN_SWAP', iterations=1, time_limit=1/1000)
mat_temp = trkr.matrix_world
# save tracker data
handler.save(mat44=[np.array(mat_temp)], pos=[np.array(mat_temp.to_translation())], rot_q=[np.array(mat_temp.to_quaternion())], frame_id=[[i]])
print (f'frame {i} data saved')
bpy.ops.render.render(write_still=True) # render still
finally:
scene.render.filepath = fp
print ('data grab done')
return {'FINISHED'}
def process_filelist_train(filelist=None,
testartists=None,
tmpfilename=None,
npicks=None,
winsize=None,
finaldim=None,
typecompress='picks'):
"""
Main function, process all files in the list (as long as their artist
is not in testartist)
INPUT
filelist - a list of song files
testartists - set of artist ID that we should not use
tmpfilename - where to save our processed features
npicks - number of segments to pick per song
winsize - size of each segment we pick
finaldim - how many values do we keep
typecompress - one of 'picks' (win of btchroma), 'corrcoef' (correlation coefficients),
'cov' (covariance)
"""
# sanity check
for arg in locals().values():
assert not arg is None, 'process_filelist_train, missing an argument, something still None'
if os.path.isfile(tmpfilename):
print 'ERROR: file', tmpfilename, 'already exists.'
return
# create outputfile
output = tables.openFile(tmpfilename, mode='a')
group = output.createGroup("/", 'data', 'TMP FILE FOR YEAR RECOGNITION')
output.createEArray(group,
'feats',
tables.Float64Atom(shape=()), (0, finaldim),
'',
expectedrows=len(filelist))
output.createEArray(group,
'year',
tables.IntAtom(shape=()), (0, ),
'',
expectedrows=len(filelist))
output.createEArray(group,
'track_id',
tables.StringAtom(18, shape=()), (0, ),
'',
expectedrows=len(filelist))
# random projection
ndim = 12 # fixed in this dataset
if typecompress == 'picks':
randproj = RANDPROJ.proj_point5(ndim * winsize, finaldim)
elif typecompress == 'corrcoeff' or typecompress == 'cov':
randproj = RANDPROJ.proj_point5(ndim * ndim, finaldim)
elif typecompress == 'avgcov':
randproj = RANDPROJ.proj_point5(90, finaldim)
else:
assert False, 'Unknown type of compression: ' + str(typecompress)
# iterate over files
cnt_f = 0
for f in filelist:
cnt_f += 1
# verbose
if cnt_f % 50000 == 0:
print 'training... checking file #', cnt_f
# check file
h5 = GETTERS.open_h5_file_read(f)
artist_id = GETTERS.get_artist_id(h5)
year = GETTERS.get_year(h5)
track_id = GETTERS.get_track_id(h5)
h5.close()
if year <= 0 or artist_id in testartists:
continue
# we have a train artist with a song year, we're good
bttimbre = get_bttimbre(f)
if typecompress == 'picks':
if bttimbre is None:
continue
# we even have normal features, awesome!
processed_feats = CBTF.extract_and_compress(bttimbre,
npicks,
winsize,
finaldim,
randproj=randproj)
elif typecompress == 'corrcoeff':
h5 = GETTERS.open_h5_file_read(f)
timbres = GETTERS.get_segments_timbre(h5).T
h5.close()
processed_feats = CBTF.corr_and_compress(timbres,
finaldim,
randproj=randproj)
elif typecompress == 'cov':
h5 = GETTERS.open_h5_file_read(f)
timbres = GETTERS.get_segments_timbre(h5).T
h5.close()
processed_feats = CBTF.cov_and_compress(timbres,
finaldim,
randproj=randproj)
elif typecompress == 'avgcov':
h5 = GETTERS.open_h5_file_read(f)
timbres = GETTERS.get_segments_timbre(h5).T
h5.close()
processed_feats = CBTF.avgcov_and_compress(timbres,
finaldim,
randproj=randproj)
else:
assert False, 'Unknown type of compression: ' + str(typecompress)
# save them to tmp file
n_p_feats = processed_feats.shape[0]
output.root.data.year.append(np.array([year] * n_p_feats))
output.root.data.track_id.append(np.array([track_id] * n_p_feats))
output.root.data.feats.append(processed_feats)
# we're done, close output
output.close()
return
sys.exit()
climb_file_paths = sys.argv[1]
climb_merge_file = sys.argv[2]
control_file_paths = sys.argv[3]
control_merge_file = sys.argv[4]
climb_files = sorted([line.strip() for line in open(climb_file_paths)])
control_files = sorted([line.strip() for line in open(control_file_paths)])
assert len(climb_files) == len(control_files)
with tables.open_file(control_merge_file, 'w') as control_merge_file:
control_liks = tables.EArray(control_merge_file.root,
'control_liks',
tables.IntAtom(),
shape=(0, ))
tot_liks = tables.EArray(control_merge_file.root,
'tot_liks',
tables.IntAtom(),
shape=(0, ))
for fname in control_files:
print("Merging", fname)
with tables.open_file(fname, 'r') as f:
control_liks.append(f.root.control_liks[:])
tot_liks.append(f.root.tot_liks[:])
with tables.open_file(climb_merge_file, 'w') as climb_merge_file:
ancs = tables.EArray(climb_merge_file.root,
'ancs',
# Open a file in "w"rite mode
fileh = tables.open_file("MDobjects.h5", mode="w")
# Create the table with compression 'on' in order to reduce size as
# much as possible
table = fileh.create_table(fileh.root,
'table',
Particle,
"A table",
filters=tables.Filters(complevel=1))
# Append several rows with default values
for i in range(10):
table.row.append()
table.flush()
# create new arrays
atom1 = tables.IntAtom()
shape1 = (2, 10, 10, 1)
filters1 = tables.Filters(complevel=1)
#(2, 10, 10, 3)
array1 = fileh.create_carray(fileh.root,
'array1',
atom1,
shape1,
filters=filters1)
atom2 = tables.FloatAtom()
shape2 = (2, 10, 10, 3, 1)
filters2 = tables.Filters(complevel=1)
#(2, 10, 10, 3, 200)
array2 = fileh.create_carray(fileh.root,
'array2',
atom2,
def create_all_arrays(h5, expectedrows=1000):
"""
Utility functions used by both create_song_file and create_aggregate_files,
creates all the EArrays (empty).
INPUT
h5 - hdf5 file, open with write or append permissions
metadata and analysis groups already exist!
"""
# group metadata arrays
group = h5.root.metadata
h5.createEArray(where=group,
name='similar_artists',
atom=tables.StringAtom(20, shape=()),
shape=(0, ),
title=ARRAY_DESC_SIMILAR_ARTISTS)
h5.createEArray(group,
'artist_terms',
tables.StringAtom(256, shape=()), (0, ),
ARRAY_DESC_ARTIST_TERMS,
expectedrows=expectedrows * 40)
h5.createEArray(group,
'artist_terms_freq',
tables.Float64Atom(shape=()), (0, ),
ARRAY_DESC_ARTIST_TERMS_FREQ,
expectedrows=expectedrows * 40)
h5.createEArray(group,
'artist_terms_weight',
tables.Float64Atom(shape=()), (0, ),
ARRAY_DESC_ARTIST_TERMS_WEIGHT,
expectedrows=expectedrows * 40)
# group analysis arrays
group = h5.root.analysis
h5.createEArray(where=group,
name='segments_start',
atom=tables.Float64Atom(shape=()),
shape=(0, ),
title=ARRAY_DESC_SEGMENTS_START)
h5.createEArray(group,
'segments_confidence',
tables.Float64Atom(shape=()), (0, ),
ARRAY_DESC_SEGMENTS_CONFIDENCE,
expectedrows=expectedrows * 300)
h5.createEArray(group,
'segments_pitches',
tables.Float64Atom(shape=()), (0, 12),
ARRAY_DESC_SEGMENTS_PITCHES,
expectedrows=expectedrows * 300)
h5.createEArray(group,
'segments_timbre',
tables.Float64Atom(shape=()), (0, 12),
ARRAY_DESC_SEGMENTS_TIMBRE,
expectedrows=expectedrows * 300)
h5.createEArray(group,
'segments_loudness_max',
tables.Float64Atom(shape=()), (0, ),
ARRAY_DESC_SEGMENTS_LOUDNESS_MAX,
expectedrows=expectedrows * 300)
h5.createEArray(group,
'segments_loudness_max_time',
tables.Float64Atom(shape=()), (0, ),
ARRAY_DESC_SEGMENTS_LOUDNESS_MAX_TIME,
expectedrows=expectedrows * 300)
h5.createEArray(group,
'segments_loudness_start',
tables.Float64Atom(shape=()), (0, ),
ARRAY_DESC_SEGMENTS_LOUDNESS_START,
expectedrows=expectedrows * 300)
h5.createEArray(group,
'sections_start',
tables.Float64Atom(shape=()), (0, ),
ARRAY_DESC_SECTIONS_START,
expectedrows=expectedrows * 300)
h5.createEArray(group,
'sections_confidence',
tables.Float64Atom(shape=()), (0, ),
ARRAY_DESC_SECTIONS_CONFIDENCE,
expectedrows=expectedrows * 300)
h5.createEArray(group,
'beats_start',
tables.Float64Atom(shape=()), (0, ),
ARRAY_DESC_BEATS_START,
expectedrows=expectedrows * 300)
h5.createEArray(group,
'beats_confidence',
tables.Float64Atom(shape=()), (0, ),
ARRAY_DESC_BEATS_CONFIDENCE,
expectedrows=expectedrows * 300)
h5.createEArray(group,
'bars_start',
tables.Float64Atom(shape=()), (0, ),
ARRAY_DESC_BARS_START,
expectedrows=expectedrows * 300)
h5.createEArray(group,
'bars_confidence',
tables.Float64Atom(shape=()), (0, ),
ARRAY_DESC_BARS_CONFIDENCE,
expectedrows=expectedrows * 300)
h5.createEArray(group,
'tatums_start',
tables.Float64Atom(shape=()), (0, ),
ARRAY_DESC_TATUMS_START,
expectedrows=expectedrows * 300)
h5.createEArray(group,
'tatums_confidence',
tables.Float64Atom(shape=()), (0, ),
ARRAY_DESC_TATUMS_CONFIDENCE,
expectedrows=expectedrows * 300)
# group musicbrainz arrays
group = h5.root.musicbrainz
h5.createEArray(where=group,
name='artist_mbtags',
atom=tables.StringAtom(256, shape=()),
shape=(0, ),
title=ARRAY_DESC_ARTIST_MBTAGS,
expectedrows=expectedrows * 5)
h5.createEArray(group,
'artist_mbtags_count',
tables.IntAtom(shape=()), (0, ),
ARRAY_DESC_ARTIST_MBTAGS_COUNT,
expectedrows=expectedrows * 5)
def opensourcefile(k, filename=None, sourcetype=None, overwrite=False):
"""Open the source term hdf5 file with filename."""
import tables
#Set up file for results
if not filename or not os.path.isdir(os.path.dirname(filename)):
source_logger.info("File or path to file %s does not exist." %
filename)
date = time.strftime("%Y%m%d%H%M%S")
filename = os.path.join(os.getcwd(), "src" + date + ".hf5")
source_logger.info("Saving source results in file " + filename)
if not sourcetype:
raise TypeError(
"Need to specify filename and type of source data to store [int(egrand)|(full)term]!"
)
if sourcetype in ["int", "term"]:
sarrname = "source" + sourcetype
if _debug:
source_logger.debug("Source array type: " + sarrname)
else:
raise TypeError("Incorrect source type specified!")
#Check if file exists and set write flags depending on overwrite option
if os.path.isfile(filename):
if overwrite:
source_logger.info("File %s exists and will be overwritten." %
filename)
writeflag = "w"
else:
source_logger.info("File %s exists and results will be appended." %
filename)
writeflag = "a"
else:
writeflag = "w"
#Add compression to files and specify good chunkshape
filters = tables.Filters(complevel=1, complib=configuration.hdf5complib)
#cshape = (10,10,10) #good mix of t, k, q values
#Get atom shape for earray
atomshape = (0, len(k))
try:
if _debug:
source_logger.debug("Trying to open source file " + filename)
rf = tables.openFile(filename, writeflag, "Source term result")
if not "results" in rf.root:
if _debug:
source_logger.debug("Creating group 'results' in source file.")
resgrp = rf.createGroup(rf.root, "results", "Results")
else:
resgrp = rf.root.results
if not sarrname in resgrp:
if _debug:
source_logger.debug("Creating array '" + sarrname +
"' in source file.")
sarr = rf.createEArray(resgrp,
sarrname,
tables.ComplexAtom(itemsize=16),
atomshape,
filters=filters)
karr = rf.createEArray(resgrp,
"k",
tables.Float64Atom(), (0, ),
filters=filters)
narr = rf.createEArray(resgrp,
"nix",
tables.IntAtom(), (0, ),
filters=filters)
karr.append(k)
else:
if _debug:
source_logger.debug(
"Source file and node exist. Testing source node shape...")
sarr = rf.getNode(resgrp, sarrname)
narr = rf.getNode(resgrp, "nix")
if sarr.shape[1:] != atomshape[1:]:
raise ValueError("Source node on file is not correct shape!")
except IOError:
raise
return rf, sarr, narr
sequence_features=sequence_features)
return contexts, features
dataset = TFRecordDataset(files)
dataset = dataset.map(_parse_function)
iterator = dataset.make_one_shot_iterator()
data_shape = (0, )
labels_shape = (0, )
sound_dtype = tables.StringAtom(itemsize=128)
labels_dtype = tables.IntAtom()
data_storage = hdf5_file.create_earray(hdf5_file.root,
'audio_embedding',
sound_dtype,
shape=data_shape)
labels_storage = hdf5_file.create_earray(hdf5_file.root,
'labels',
labels_dtype,
shape=labels_shape)
value = iterator.get_next()
i = 1
with tf.Session() as sess:
while 1:
try:
climb_lik_file = '/RQusagers/dnelson/project/anc_finder/results/BALSAC/CAID_3M_all_anc_out.csv'
max_trees = 1000
print "Loading climbing likelihoods"
climb_liks = np.genfromtxt(climb_lik_file,
skip_header=True,
delimiter=',',
usecols=[1])[:max_trees]
print "Loading trees"
trees = [line.strip() for line in open(tree_anc_file, 'r')][:max_trees]
climb_outfile = os.path.expanduser('~/temp/CAID_climb_1000.h5')
with tables.open_file(climb_outfile, 'w') as f:
## Create extendable arrays so we can incrementally write output
f.create_earray(f.root, 'liks', atom=tables.FloatAtom(), shape=(0, ))
f.create_earray(f.root, 'ancs', atom=tables.FloatAtom(), shape=(0, ))
## Trees, which are variable-length, must be added individually
f.create_vlarray(f.root, 'trees', atom=tables.IntAtom())
f.create_vlarray(f.root, 'genotypes', atom=tables.IntAtom())
incremental_write(climb_liks, trees, climb_outfile)
## Store control likelihoods
# control_outfile = os.path.expanduser('~/temp/CAID_control.h5')
#
# init_array(control_outfile, array_name='control_liks')
# with tables.open_file(control_outfile, 'a') as f:
# f.root.control_liks.append([np.log2(conv_prob)])
def process_filelist_test(filelist=None,
model=None,
tmpfilename=None,
npicks=None,
winsize=None,
finaldim=None,
K=1,
typecompress='picks'):
"""
Main function, process all files in the list (as long as their artist
is in testartist)
INPUT
filelist - a list of song files
model - h5 file containing feats and year for all train songs
tmpfilename - where to save our processed features
npicks - number of segments to pick per song
winsize - size of each segment we pick
finaldim - how many values do we keep
K - param of KNN (default 1)
typecompress - feature type, 'picks', 'corrcoeff' or 'cov'
must be the same as in training
"""
# sanity check
for arg in locals().values():
assert not arg is None, 'process_filelist_test, missing an argument, something still None'
if os.path.isfile(tmpfilename):
print 'ERROR: file', tmpfilename, 'already exists.'
return
if not os.path.isfile(model):
print 'ERROR: model', model, 'does not exist.'
return
# create kdtree
h5model = tables.openFile(model, mode='r')
assert h5model.root.data.feats.shape[
1] == finaldim, 'inconsistency in final dim'
kd = ANN.kdtree(h5model.root.data.feats)
# create outputfile
output = tables.openFile(tmpfilename, mode='a')
group = output.createGroup("/", 'data', 'TMP FILE FOR YEAR RECOGNITION')
output.createEArray(group,
'year_real',
tables.IntAtom(shape=()), (0, ),
'',
expectedrows=len(filelist))
output.createEArray(group,
'year_pred',
tables.Float64Atom(shape=()), (0, ),
'',
expectedrows=len(filelist))
# random projection
ndim = 12 # fixed in this dataset
if typecompress == 'picks':
randproj = RANDPROJ.proj_point5(ndim * winsize, finaldim)
elif typecompress == 'corrcoeff' or typecompress == 'cov':
randproj = RANDPROJ.proj_point5(ndim * ndim, finaldim)
elif typecompress == 'avgcov':
randproj = RANDPROJ.proj_point5(90, finaldim)
else:
assert False, 'Unknown type of compression: ' + str(typecompress)
# go through files
cnt_f = 0
for f in filelist:
cnt_f += 1
if cnt_f % 5000 == 0:
print 'TESTING FILE #' + str(cnt_f)
# check file
h5 = GETTERS.open_h5_file_read(f)
artist_id = GETTERS.get_artist_id(h5)
year = GETTERS.get_year(h5)
track_id = GETTERS.get_track_id(h5)
h5.close()
if year <= 0: # probably useless but...
continue
if typecompress == 'picks':
# we have a train artist with a song year, we're good
bttimbre = get_bttimbre(f)
if bttimbre is None:
continue
# we even have normal features, awesome!
processed_feats = CBTF.extract_and_compress(bttimbre,
npicks,
winsize,
finaldim,
randproj=randproj)
elif typecompress == 'corrcoeff':
h5 = GETTERS.open_h5_file_read(f)
timbres = GETTERS.get_segments_timbre(h5).T
h5.close()
processed_feats = CBTF.corr_and_compress(timbres,
finaldim,
randproj=randproj)
elif typecompress == 'cov':
h5 = GETTERS.open_h5_file_read(f)
timbres = GETTERS.get_segments_timbre(h5).T
h5.close()
processed_feats = CBTF.cov_and_compress(timbres,
finaldim,
randproj=randproj)
elif typecompress == 'avgcov':
h5 = GETTERS.open_h5_file_read(f)
timbres = GETTERS.get_segments_timbre(h5).T
h5.close()
processed_feats = CBTF.avgcov_and_compress(timbres,
finaldim,
randproj=randproj)
else:
assert False, 'Unknown type of compression: ' + str(typecompress)
if processed_feats is None:
continue
if processed_feats.shape[0] == 0:
continue
# do prediction
year_pred = do_prediction(processed_feats, kd, h5model, K)
# add pred and ground truth to output
if not year_pred is None:
output.root.data.year_real.append([year])
output.root.data.year_pred.append([year_pred])
# close output and model
del kd
h5model.close()
output.close()
# done
return
def initialize_database(self, **kargs):
"""
Initializes the EventDatabase. Adds a group 'events' with
table 'eventsTable' and matrices 'raw_data', 'levels', and 'level_lengths'.
:param kargs: Dictionary - includes:
-maxEventLength: Maximum number of datapoints for an event to be added.
"""
if 'maxEventLength' in kargs:
if kargs['maxEventLength'] > self.max_event_length:
self.max_event_length = kargs['maxEventLength']
if 'events' not in self.root:
self.createGroup(self.root, 'events', 'Events')
if not 'eventTable' in self.root.events:
self.createTable(self.root.events, 'eventTable', _Event,
'Event parameters')
self.event_row = None
filters = tb.Filters(complib='blosc', complevel=4)
shape = (0, self.max_event_length)
a = tb.FloatAtom()
b = tb.IntAtom()
if not 'raw_data' in self.root.events:
self.createEArray(self.root.events,
'raw_data',
a,
shape=shape,
title="Raw data points",
filters=filters)
if not 'levels' in self.root.events:
self.createEArray(self.root.events,
'levels',
a,
shape=shape,
title="Cusum levels",
filters=filters)
if not 'level_lengths' in self.root.events:
self.createEArray(self.root.events,
'level_lengths',
b,
shape=shape,
title="Lengths of the cusum levels",
filters=filters)
# Create/init the debug group if needed.
if 'debug' in kargs and kargs['debug']:
if not 'debug' in self.root:
self.createGroup(self.root, 'debug', 'Debug')
debug_shape = (kargs['n_channels'], kargs['n_points'])
if not 'data' in self.root.debug:
self.createCArray(self.root.debug,
'data',
a,
shape=debug_shape,
title="Raw data",
filters=filters)
if not 'baseline' in self.root.debug:
self.createCArray(self.root.debug,
'baseline',
a,
shape=debug_shape,
title="Baseline data",
filters=filters)
if not 'threshold_positive' in self.root.debug:
self.createCArray(self.root.debug,
'threshold_positive',
a,
shape=debug_shape,
title="Raw data",
filters=filters)
if not 'threshold_negative' in self.root.debug:
self.createCArray(self.root.debug,
'threshold_negative',
a,
shape=debug_shape,
title="Raw data",
filters=filters)
def create_hdf_arrays(file_name,
rec_info,
electrode_mapping,
emg_mapping,
file_dir=None):
'''Creates empty data arrays in hdf5 store for storage of the intan
recording data.
Parameters
----------
file_name : str, absolute path to h5 file
rec_info : dict
recording info dict provided by blechpy.rawIO.read_recording_info
electrode_mapping : pandas.DataFrame
with colummns Electrode, Port and Channels
emg_mapping : pandas.Dataframe
with columns EMG, Port and Channels (can be empty)
file_dir : str (optional)
path to recording directory if h5 is in different folder
Throws
------
ValueError
if file_name is not absolute path to file and file_dir is not provided
'''
if file_dir is None:
file_dir = os.path.dirname(file_name)
if file_dir is '':
raise ValueError(('Must provide absolute path to file in a recording'
'directory or a file_dir argument'))
if not os.path.isabs(file_name):
file_name = os.path.join(file_dir, file_name)
println('Creating empty arrays in hdf5 store for raw data...')
sys.stdout.flush()
atom = tables.IntAtom()
f_atom = tables.Float64Atom()
with tables.open_file(file_name, 'r+') as hf5:
# Create array for raw time vector
hf5.create_earray('/raw', 'amplifier_time', f_atom, (0, ))
# Create arrays for each electrode
for idx, row in electrode_mapping.iterrows():
hf5.create_earray('/raw', 'electrode%i' % row['Electrode'], atom,
(0, ))
# Create arrays for raw emg (if any exist)
if not emg_mapping.empty:
for idx, row in emg_mapping:
hf5.create_earray('/raw_emg', 'emg%i' % row['EMG'], atom,
(0, ))
# Create arrays for digital inputs (if any exist)
if rec_info.get('dig_in'):
for x in rec_info['dig_in']:
hf5.create_earray('/digital_in', 'dig_in_%i' % x, atom, (0, ))
# Create arrays for digital outputs (if any exist)
if rec_info.get('dig_out'):
for x in rec_info['dig_out']:
hf5.create_earray('/digital_out', 'dig_out_%i' % x, atom,
(0, ))
print('Done!')
def generate_per_subject_cache(xls_data, test_split=0.3, validation_split=0.3):
prevElem = None
h5file = tb.openFile(FULL_SPECTROGRAM_BY_SUBJECT_CACHE,
mode='w',
title="All the data")
root = h5file.root
first = True
X_train = None
Y_train = None
X_validate = None
Y_validate = None
X_test = None
Y_test = None
y_append = None
X_append = None
for ss_id, regions_of_interest in xls_data.items():
avi = maybe_get_unique_avi_from_subjectState_id(ss_id)
if avi:
#split the subjects into vlaidation, train and test sets
ran_num = random.uniform(0, 1)
if ran_num < test_split:
X_append, y_append = X_test, Y_test
elif ran_num < test_split + validation_split:
X_append, y_append = X_validate, Y_validate
else:
X_append, y_append = X_train, Y_train
sw = SubjectVideo(avi)
for _, timestamp, bpm in regions_of_interest:
#reduces the memory used - for testing
#if random.uniform(0,1) < 0.9:
# continue
timestamp = int(timestamp)
bpm = round(float(bpm))
try:
_, _, Sxx0 = sw.get_spectrogram(timestamp, 4)
#workaround this error
# max_freq_idx = int((max_freqency / f[-1]) * Sxx.shape[0])
#IndexError: index -1 is out of bounds for axis 0 with size 0
except IndexError:
print("Something went wrong for avi, timestamp ", avi,
timestamp)
continue
elem = np.array([Sxx0])
if prevElem is not None and elem.shape != prevElem.shape:
print("skipping " + str(avi) + " " + ss_id +
" due to incorrect shape")
continue
prevElem = elem
#store the elem to disk
if first:
first = False
a = tb.Atom.from_dtype(np.dtype('Float32'))
data_shape = tuple([0] + list(elem.shape))
X_train = h5file.create_earray(root, 'X_train', a,
data_shape, "X_train")
X_test = h5file.create_earray(root, 'X_test', a,
data_shape, "X_test")
X_validate = h5file.create_earray(root, 'X_validate', a,
data_shape, "X_validate")
Y_train = h5file.create_earray(root, 'Y_train',
tb.IntAtom(), (0, ),
"Y_train")
Y_test = h5file.create_earray(root, 'Y_test', tb.IntAtom(),
(0, ), "Y_test")
Y_validate = h5file.create_earray(root, 'Y_validate',
tb.IntAtom(), (0, ),
"Y_validate")
X_append, y_append = X_test, Y_test
X_append.append(np.array([elem]))
y_append.append([bpm])
h5file.flush()
print("converted " + str(avi) + " for " + X_append.title + " set")
else:
print("Skipping " + ss_id + " becuase it isn't unique")
h5file.close()
def bpm_to_data(data, train_split=0.9):
try:
return readh5File(SPECTROGRAM_CACHE)
except IOError:
pass
pattern = re.compile(".*vp_(\\d+)_(\\d+)_.*")
prevElem = None
# limit = 250
h5file = tb.openFile(SPECTROGRAM_CACHE, mode='w', title="All the data")
root = h5file.root
first = True
X_train = None
Y_train = None
X_test = None
Y_test = None
for wavFile in iterateThroughWav():
m = pattern.match(wavFile)
subjectId = int(m.group(1))
stateId = int(m.group(2))
sw = SubjectWav(wavFile)
subjectStateId = str(subjectId) + "_" + str(stateId).zfill(2)
try:
for _, timestamp, bpm in data[subjectStateId]:
#reduces the memory used
# if random.uniform(0,1) < 0.9:
# continue
timestamp = int(timestamp)
bpm = round(float(bpm))
_, _, Sxx0 = sw.get_spectrogram(timestamp, 4)
# print(Sxx0.shape) #(651,154) (801,219)
elem = np.array([Sxx0])
if prevElem is not None and elem.shape != prevElem.shape:
print("skipping " + str(wavFile) + " " + subjectStateId +
" due to incorrect shape")
continue
prevElem = elem
#store the elem to disk
if first:
first = False
a = tb.Atom.from_dtype(np.dtype('Float32'))
data_shape = tuple([0] + list(elem.shape))
X_train = h5file.create_earray(root, 'X_train', a,
data_shape, "X_train")
X_test = h5file.create_earray(root, 'X_test', a,
data_shape, "X_test")
Y_train = h5file.create_earray(root, 'Y_train',
tb.IntAtom(), (0, ),
"Y_train")
# code.interact(local=locals())
Y_test = h5file.create_earray(root, 'Y_test', tb.IntAtom(),
(0, ), "Y_test")
if random.uniform(0, 1) < 0.9:
X_train.append(np.array([elem]))
Y_train.append([bpm])
else:
X_test.append(np.array([elem]))
Y_test.append([bpm])
h5file.flush()
except KeyError:
print("can not find: " + subjectStateId + ".")
pass
print("converted " + str(wavFile))
#Could not broadcast error means that not all elemnt of X_train have the same shape
#usually meaning there is something wrong with files
h5file.close()
# data = (X_train, Y_train) , (X_test, Y_test)
# write_cache(SPECTROGRAM_CACHE,data)
return readh5File(SPECTROGRAM_CACHE)
def full_bpm_to_data(data, train_split=0.9):
try:
return readh5File(FULL_SPECTROGRAM_CACHE)
except IOError:
pass
prevElem = None
h5file = tb.openFile(FULL_SPECTROGRAM_CACHE,
mode='w',
title="All the data")
root = h5file.root
first = True
X_train = None
Y_train = None
X_test = None
Y_test = None
for ss_id, regions_of_interest in data.items():
avi = maybe_get_unique_avi_from_subjectState_id(ss_id)
if avi:
sw = SubjectVideo(avi)
for _, timestamp, bpm in regions_of_interest:
#reduces the memory used
# if random.uniform(0,1) < 0.9:
# continue
timestamp = int(timestamp)
bpm = round(float(bpm))
try:
_, _, Sxx0 = sw.get_spectrogram(timestamp, 4)
#workaround this error
# max_freq_idx = int((max_freqency / f[-1]) * Sxx.shape[0])
#IndexError: index -1 is out of bounds for axis 0 with size 0
except IndexError:
print("Something went wrong for avi, timestamp ", avi,
timestamp)
continue
elem = np.array([Sxx0])
if prevElem is not None and elem.shape != prevElem.shape:
print("skipping " + str(avi) + " " + ss_id +
" due to incorrect shape")
continue
prevElem = elem
#store the elem to disk
if first:
first = False
a = tb.Atom.from_dtype(np.dtype('Float32'))
data_shape = tuple([0] + list(elem.shape))
X_train = h5file.create_earray(root, 'X_train', a,
data_shape, "X_train")
X_test = h5file.create_earray(root, 'X_test', a,
data_shape, "X_test")
Y_train = h5file.create_earray(root, 'Y_train',
tb.IntAtom(), (0, ),
"Y_train")
Y_test = h5file.create_earray(root, 'Y_test', tb.IntAtom(),
(0, ), "Y_test")
if random.uniform(0, 1) < train_split:
X_train.append(np.array([elem]))
Y_train.append([bpm])
else:
X_test.append(np.array([elem]))
Y_test.append([bpm])
h5file.flush()
print("converted " + str(avi))
else:
print("Skipping " + ss_id + " becuase it isn't unique")
h5file.close()
return readh5File(FULL_SPECTROGRAM_CACHE)
def train(nthreads,
maindir,
output,
testartists,
npicks,
winsize,
finaldim,
trainsongs=None,
typecompress='picks'):
"""
Main function to do the training
Do the main pass with the number of given threads.
Then, reads the tmp files, creates the main output, delete the tmpfiles.
INPUT
- nthreads - number of threads to use
- maindir - dir of the MSD, wehre to find song files
- output - main model, contains everything to perform KNN
- testartists - set of artists to ignore
- npicks - number of samples to pick per song
- winsize - window size (in beats) of a sample
- finaldim - final dimension of the sample, something like 5?
- trainsongs - list of songs to use for training
- typecompress - 'picks', 'corrcoeff' or 'cov'
RETURN
- nothing
"""
# sanity checks
if os.path.isfile(output):
print 'ERROR: file', output, 'already exists.'
return
# initial time
t1 = time.time()
# do main pass
tmpfiles = process_filelist_train_main_pass(nthreads,
maindir,
testartists,
npicks,
winsize,
finaldim,
trainsongs=trainsongs,
typecompress=typecompress)
if tmpfiles is None:
print 'Something went wrong, tmpfiles are None'
return
# intermediate time
t2 = time.time()
stimelen = str(datetime.timedelta(seconds=t2 - t1))
print 'Main pass done after', stimelen
sys.stdout.flush()
# find approximate number of rows per tmpfiles
h5 = tables.openFile(tmpfiles[0], 'r')
nrows = h5.root.data.year.shape[0] * len(tmpfiles)
h5.close()
# create output
output = tables.openFile(output, mode='a')
group = output.createGroup("/", 'data',
'KNN MODEL FILE FOR YEAR RECOGNITION')
output.createEArray(group,
'feats',
tables.Float64Atom(shape=()), (0, finaldim),
'feats',
expectedrows=nrows)
output.createEArray(group,
'year',
tables.IntAtom(shape=()), (0, ),
'year',
expectedrows=nrows)
output.createEArray(group,
'track_id',
tables.StringAtom(18, shape=()), (0, ),
'track_id',
expectedrows=nrows)
# aggregate temp files
for tmpf in tmpfiles:
h5 = tables.openFile(tmpf)
output.root.data.year.append(h5.root.data.year[:])
output.root.data.track_id.append(h5.root.data.track_id[:])
output.root.data.feats.append(h5.root.data.feats[:])
h5.close()
# delete tmp file
os.remove(tmpf)
# close output
output.close()
# final time
t3 = time.time()
stimelen = str(datetime.timedelta(seconds=t3 - t1))
print 'Whole training done after', stimelen
# done
return