def show(config, path, stack, timepoint):
"""Preview MIPS or single Z stack from LLSdir"""
from llspy.gui.img_dialog import ImgDialog
from PyQt5 import QtWidgets
import numpy as np
logging.getLogger('llspy.llsdir').setLevel('CRITICAL')
APP = QtWidgets.QApplication(sys.argv)
# if the path provided is a tiff, just show it
if os.path.isfile(path) and path.endswith('.tif'):
data = util.imread(path)
if os.path.isdir(path) and util.pathHasPattern(path, '*Settings.txt'):
try:
data = None
exp = llsdir.LLSdir(path)
# unless z-stack was requested, look for mips
if not stack:
# look for decon first, then deskewed
if exp.path.joinpath('GPUdecon').joinpath('MIPs').exists():
path = exp.path.joinpath('GPUdecon').joinpath('MIPs')
zmip = util.find_filepattern(path, '*comboMIP_z.tif')
data = util.imread(zmip)
nt, ny, nx = data.shape
data = np.reshape(data, (nt, 1, 1, ny, nx))
elif exp.path.joinpath('Deskewed').joinpath('MIPs').exists():
path = exp.path.joinpath('Deskewed').joinpath('MIPs')
zmip = util.find_filepattern(path, '*comboMIP_z.tif')
data = util.imread(zmip)
nt, ny, nx = data.shape
data = np.reshape(data, (nt, 1, 1, ny, nx))
if data is None:
data = exp.preview(tR=timepoint, **config)
config = exp.localParams()
except exceptions.ParametersError as e:
click.secho(str(e), fg='red')
click.echo('Try setting missing parameters using "lls config"')
return
dialog = ImgDialog(data, info=config)
dialog.show()
sys.exit(APP.exec_())
def processFolder(self):
folder = self.camCalibFolderLineEdit.text()
darkavg = None
if os.path.isfile(self.darkAVGLineEdit.text()):
darkavg = tf.imread(self.darkAVGLineEdit.text())
elif os.path.isfile(os.path.join(folder, 'dark_AVG.tif')):
darkavg = tf.imread(os.path.join(folder, 'dark_AVG.tif'))
darkstd = None
if os.path.isfile(self.darkSTDLineEdit.text()):
darkstd = tf.imread(self.darkSTDLineEdit.text())
elif os.path.isfile(os.path.join(folder, 'dark_STD.tif')):
darkstd = tf.imread(os.path.join(folder, 'dark_STD.tif'))
if not all([isinstance(a, np.ndarray) for a in (darkavg, darkstd)]):
if not pathHasPattern(folder, '*dark*.tif*'):
QtW.QMessageBox.warning(
self, "No dark images!",
'Camera calibration requires dark images, but none were provided'
' and none were detected in the specified folder.'
' Read documentation on camera calibration for more info.',
QtW.QMessageBox.Ok, QtW.QMessageBox.NoButton)
return
if sum([isinstance(a, np.ndarray) for a in (darkavg, darkstd)]) == 1:
if not pathHasPattern(folder, '*dark*.tif*'):
QtW.QMessageBox.warning(
self, "No dark images!",
'Camera calibration requires both a dark image average projection, '
' and a standard deviation projection, but only one of the'
' two was provided, and no *dark*.tif images '
' were detected in the specified folder.'
' Read documentation on camera calibration for more info.',
QtW.QMessageBox.Ok, QtW.QMessageBox.NoButton)
return
else:
reply = QtW.QMessageBox.question(
self, "No dark images!",
'Camera calibration requires both a dark image average projection, '
' and a standard deviation projection, but only one of the'
' two was provided. *dark*.tif images '
' were detected in the specified folder, and will still be '
' used to calculate the projection images. Continue?',
QtW.QMessageBox.Yes | QtW.QMessageBox.No,
QtW.QMessageBox.No)
if reply != QtW.QMessageBox.Yes:
return
self.worker, self.thread = newWorkerThread(
CamCalibWorker,
folder,
darkavg,
darkstd,
workerConnect={
'progress': self.incrementProgress,
'setProgMax': self.resetWithMax,
'setStatus': self.statusLabel.setText,
'finished': self.abortButton.hide,
},
start=True)
def decon(config, path, **kwargs):
"""Deskew and deconvolve data in LLSDIR."""
# update config with relevant values from
# raw deskewed MIPs imply saving Deskewed Raw files
if any(kwargs['rMIP']):
kwargs['saveDeskewedRaw'] = True
# override config with keyword options
for key, value in kwargs.items():
if key in config and value is not None:
config[key] = value
# batch processing
if not kwargs['batch'] and not util.pathHasPattern(path):
click.secho(
'not a LLS data folder with *Settings.txt!\n'
'use --batch for batch processing',
fg='red')
sys.exit(1)
# # allow for provided OTF directory
# if not default_otfdir and options.otfdir is None:
# print('Could not find OTF directory at {}'.format(default_otfdir))
# sys.exit('Please specify where the OTFs are with --otfdir')
# elif options.otfdir is None:
# options.otfdir = default_otfdir
def procfolder(dirpath, options):
E = llsdir.LLSdir(dirpath)
# check whether folder has already been processed by the presence of a
# ProcessingLog.txt file
if E.has_been_processed() and not options['reprocess']:
print("Folder already appears to be processed: {}".format(E.path))
print(
"Skipping ... use the '--reprocess' flag to force reprocessing"
)
return 0
if options['reprocess'] and E.is_compressed():
# uncompress the raw files first...
E.decompress()
# if reprocessing, look for a top level MIPs folder and remove it
if E.path.joinpath('MIPs').exists():
shutil.rmtree(E.path.joinpath('MIPs'))
click.secho("\n" + "#" * (int(len(str(E.path))) + 24) + "\n## ",
fg='cyan',
nl=False)
click.secho("processing: %s " % str(E.path), fg='yellow', nl=False)
click.secho("##\n" + "#" * (int(len(str(E.path))) + 24) + "\n",
fg='cyan')
if options['correctFlash']:
if E.is_corrected():
if kwargs['useAlreadyCorrected'] is None:
import select
click.echo(
"Corrected folder already exists! Use it? [y/N]",
nl=False)
click.secho(" (6 seconds to answer)", blink=True)
i, o, e = select.select([sys.stdin], [], [], 6)
if i:
useCor = (
sys.stdin.readline().strip()[0].lower() == 'y')
else:
useCor = False
click.echo("timed out...")
elif kwargs['useAlreadyCorrected']:
useCor = True
else:
useCor = False
if useCor:
click.echo("Using already corrected files...")
options['correctFlash'] = False
E.path = E.path.joinpath('Corrected')
else:
click.echo("recreating corrected files...")
try:
# try:
E.autoprocess(**options)
# logdict = None
# except Exception as e:
# raise click.ClickException(e)
except Exception:
raise
if kwargs['batch']:
try:
subfolders = util.get_subfolders_containing_filepattern(
path, filepattern='*Settings.txt')
click.secho("found the following LLS data folders:", fg='magenta')
for folder in subfolders:
click.secho(folder.split(path)[1], fg='yellow')
for folder in subfolders:
try:
procfolder(folder, config)
except voluptuous.error.MultipleInvalid as e:
e = str(e).replace("@ data['", 'for ')
e = e.strip("'][0]")
click.secho("VALIDATION ERROR: %s" % e, fg='red')
except exceptions.LLSpyError as e:
click.secho("ERROR: %s" % e, fg='red')
click.echo('\n\nDone batch processing!')
sys.exit(0)
except Exception:
raise
else:
try:
procfolder(path, config)
click.echo('Done!')
sys.exit(0)
except voluptuous.error.MultipleInvalid as e:
e = str(e).replace("@ data['", 'for ')
e = e.strip("'][0]")
click.secho("VALIDATION ERROR: %s" % e, fg='red')
except exceptions.LLSpyError as e:
click.secho("ERROR: %s" % e, fg='red')
sys.exit(0)
def compress(paths, freeze, _reduce, decompress, recurse, minage, keepmips,
depth, dryrun):
"""Compression & decompression of LLSdir"""
exclusive(click.get_current_context().params,
['freeze', '_reduce', 'decompress'],
'options {freeze, reduce, decompress} are mutually exclusive')
logging.getLogger('llspy.llsdir').setLevel('CRITICAL')
paths = list(paths)
if recurse:
depth = 1000
# recurse and restrict to LLSdirs
for i, path in enumerate(paths):
if not util.pathHasPattern(path, pattern='*Settings.txt'):
paths.pop(i)
subf = sorted(
util.get_subfolders_containing_filepattern(path, level=depth))
[paths.insert(i, s) for s in reversed(subf)]
# remove duplicates
paths = sorted(list(set(paths)))
if dryrun:
click.secho("DRY RUN: NOTHING PERFORMED!", fg='red', underline=True)
for path in paths:
try:
E = llsdir.LLSdir(path)
if E.age < minage:
click.secho(' skip:',
nl=False,
underline=False,
fg='blue')
click.secho('{} ({} days old)'.format(path, E.age), fg='blue')
continue
if decompress:
click.secho('decompress:',
nl=False,
underline=False,
fg='yellow')
click.echo('{}'.format(path))
if not dryrun:
E.decompress()
continue
elif _reduce:
click.secho(' reduce:',
nl=False,
underline=False,
fg='yellow')
click.echo('{}'.format(path))
if not dryrun:
E.reduce_to_raw(keepmip=keepmips)
continue
else:
if freeze:
click.secho(' freeze:',
nl=False,
underline=False,
fg='yellow')
click.echo('{}'.format(path))
if not dryrun:
E.freeze(keepmip=keepmips)
else:
click.secho(' compress:',
nl=False,
underline=False,
fg='yellow')
click.echo('{}'.format(path))
if not dryrun:
E.compress()
except exceptions.CompressionError as e:
logger.warn(e)
def info(paths, verbose, recurse, depth, showsize):
"""Get info on an LLSDIR. Change verbosity with -v"""
logging.getLogger('llspy.llsdir').setLevel('CRITICAL')
paths = list(paths)
if recurse:
depth = 1000
for i, path in enumerate(paths):
if not util.pathHasPattern(path, pattern='*Settings.txt'):
paths.pop(i)
subf = sorted(
util.get_subfolders_containing_filepattern(path, level=depth))
[paths.insert(i, s) for s in reversed(subf)]
# remove duplicates
paths = sorted(list(set(paths)))
if verbose == 0 and len(paths):
click.echo()
headers = [
'Path', 'nC', 'nT', 'nZ', 'nY', 'nX', 'Angle', 'dZ', 'dXY', 'compr'
]
maxPathLen = max([len(util.shortname(str(p), 3)) for p in paths]) + 2
row_format = "{:<%d}{:<4}{:<5}{:<5}{:<6}{:<6}{:<7}{:<7}{:<7}{:<5}" % maxPathLen
if showsize:
headers.append('size')
row_format = row_format + "{:>7}"
click.secho(row_format.format(*[str(i) for i in headers]),
underline=True,
fg='cyan',
bold=True)
row_format = "{:<4}{:<5}{:<5}{:<6}{:<6}{:<7}{:<7}{:<7}{:<5}"
if showsize:
row_format = row_format + "{:>7}"
for path in paths:
try:
E = llsdir.LLSdir(path)
infolist = [
E.parameters.nc, E.parameters.nt, E.parameters.nz,
E.parameters.ny, E.parameters.nx,
"{:2.1f}".format(E.parameters.angle)
if E.parameters.samplescan else "0",
"{:0.3f}".format(E.parameters.dz),
"{:0.3f}".format(E.parameters.dx),
"Yes" if E.is_compressed() else "No"
]
if showsize:
foldersize = util.getfoldersize(path, recurse=True)
infolist.append(util.format_size(foldersize))
f = "{:<%d}" % maxPathLen
short = f.format(util.shortname(str(E.path), 3))
click.secho(os.path.split(short)[0] + os.path.sep,
nl=False,
fg='magenta',
bold=False)
click.secho(os.path.split(short)[1],
nl=False,
fg='yellow',
bold=True)
click.echo(row_format.format(*[i for i in infolist]))
except exceptions.LLSpyError:
pass
click.echo()