def stimulus_list():
return glia.load_stimulus(
"tests/data/160615/E1_R1_DAD_55min_contrastgratings.stimulus")
def stimulus_list():
return glia.load_stimulus("tests/data/160615/E1_R1_DAD_55min_contrastgratings.stimulus")
def analyze(ctx, filename, trigger, threshold, eyecandy, ignore_extra=False,
fix_missing=False, window_height=None, window_width=None, output=None, notebook=None,
calibration=None, distance=None):
"""Analyze data recorded with eyecandy.
"""
ctx.obj = {}
data_directory, data_name = os.path.split(filename)
name, extension = os.path.splitext(data_name)
analog_file = os.path.join(data_directory, name +'.analog')
stimulus_file = os.path.join(data_directory, name + ".stimulus")
spyking_regex = re.compile('.*\.result.hdf5$')
if extension == ".txt":
ctx.obj["units"] = glia.read_plexon_txt_file(filename,filename)
elif re.match(spyking_regex, filename):
ctx.obj["units"] = glia.read_spyking_results(filename)
else:
raise ValueError('could not read {}. Is it a plexon or spyking circus file?')
if not notebook:
notebooks = glob(os.path.join(data_directory, '*.yml')) + \
glob(os.path.join(data_directory, '*.yaml'))
if len(notebooks)==0:
raise ValueError("no lab notebooks (.yml) were found. Either add to directory," \
"or specify file path with -n.")
notebook=notebooks[0]
lab_notebook = glia.open_lab_notebook(notebook)
experiment_protocol = glia.get_experiment_protocol(lab_notebook, name)
flicker_version = experiment_protocol["flickerVersion"]
try:
ctx.obj["stimulus_list"] = glia.load_stimulus(stimulus_file)
except OSError:
print("No .stimulus file found. Attempting to create from .analog file.".format(trigger))
if flicker_version==0.3:
ctx.obj["stimulus_list"] = glia.create_stimulus_list_v0_4(
analog_file, stimulus_file, notebook, name, eyecandy, ignore_extra,
calibration, distance)
elif trigger == "legacy":
ctx.obj["stimulus_list"] = glia.legacy_create_stimulus_list_from_flicker(
analog_file, stimulus_file, notebook, name, eyecandy, ignore_extra, threshold, window_height, window_width)
elif trigger == "flicker":
ctx.obj["stimulus_list"] = glia.create_stimulus_list_from_flicker(
analog_file, stimulus_file, notebook, name, eyecandy, ignore_extra, threshold, fix_missing, window_height, window_width)
elif trigger == "fix":
ctx.obj["stimulus_list"] = glia.alternate_create_stimulus_list_from_flicker(
analog_file, stimulus_file, notebook, name, eyecandy, ignore_extra, threshold, window_height, window_width,
fix_missing=True)
elif trigger == "detect-solid":
ctx.obj["stimulus_list"] = glia.create_stimulus_list_from_SOLID(
analog_file, stimulus_file, notebook, name, eyecandy, ignore_extra, threshold, window_height, window_width)
elif trigger == "ttl":
raise ValueError('not implemented')
else:
raise ValueError("invalid trigger: {}".format(trigger))
# prepare_output
plot_directory = os.path.join(data_directory, name+"-plots")
try:
os.makedirs(plot_directory)
os.chmod(plot_directory, 0o777)
except OSError as exception:
if exception.errno != errno.EEXIST:
raise
if output == "pdf":
ctx.obj["retina_pdf"] = PdfPages(glia.plot_pdf_path(plot_directory, "retina"))
ctx.obj["unit_pdfs"] = glia.open_pdfs(plot_directory, list(ctx.obj["units"].keys()), Unit.name_lookup())
# c connotes 'continuation'
ctx.obj["c_add_unit_figures"] = partial(glia.add_to_unit_pdfs,
unit_pdfs=ctx.obj["unit_pdfs"])
ctx.obj["c_add_retina_figure"] = lambda x: ctx.obj["retina_pdf"].savefig(x)
elif output == "png":
raise ValueError("not implemented")