def run(self):
Hname = utils.getFilename("Select affine transformation matrix",
[('npy files', '.npy')])
H = np.load(Hname)
text = "Select files for affine transformation"
filenames = utils.getFilenames(text,
types=[],
initialdir=os.path.split(Hname)[0])
for filename in filenames:
print(
time.strftime("%Y-%m-%d %H:%M:%S") + ' Transforming stack ' +
os.path.split(filename)[1])
ext = os.path.splitext(filename)[1]
filename2 = utils.insertSuffix(filename, '_corrected')
if ext == '.hdf5':
with hdf.File(filename, 'r') as f0, \
hdf.File(filename2, 'w') as f1:
dat0 = f0['data']
xlim, ylim, cropShape = get_affine_shapes(dat0.shape, H)
print(dat0.shape)
dat1 = self.mpStack(dat0, xlim, ylim, H)
# Store
f1.create_dataset(name='data', data=dat1)
# f1['data'][:, -cropShape[0]:, :] = im1c
elif ext in ['.tiff', '.tif']:
with tiff.TiffFile(filename) as tt:
dat0 = tt.asarray()
if len(dat0.shape) > 2:
results = get_affine_shapes(dat0.shape, H)
xlim, ylim, cropShape = results
dat1 = self.mpStack(dat0, xlim, ylim, H)
tiff.imsave(filename2, dat1)
else:
sh0 = np.array(
[0.5 * dat0.shape[0] - 5, dat0.shape[1]])
sh0 = sh0.astype(np.int)
tiff.imsave(utils.insertSuffix(filename, '_ch0'),
dat0[:sh0[0], :])
tiff.imsave(utils.insertSuffix(filename, '_ch1'),
h_affine_transform(dat0[-sh0[0]:, :], H))
print(time.strftime("%Y-%m-%d %H:%M:%S") + ' done')
self.finished.emit()
def split_two_colors(files):
for name in files:
with hdf.File(name, 'r') as ff:
print(name)
center = int(0.5*ff['data'].value.shape[1])
with hdf.File(utils.insertSuffix(name, '_ch0'), 'w') as ff0:
ff0['data'] = ff['data'][:, center - 5 - 128:center - 5, :]
with hdf.File(utils.insertSuffix(name, '_ch1'), 'w') as ff1:
ff1['data'] = ff['data'][:, center + 5:center + 5 + 128, :]
def getUniqueName(name):
n = 1
while os.path.exists(name):
if n > 1:
name = name.replace('_{}.'.format(n - 1), '_{}.'.format(n))
else:
name = utils.insertSuffix(name, '_{}'.format(n))
n += 1
return name
def getUniqueName(name):
n = 1
while os.path.exists(name):
if n > 1:
name = name.replace('_{}.'.format(n - 1), '_{}.'.format(n))
else:
name = utils.insertSuffix(name, '_{}'.format(n))
n += 1
return name
def run(self):
txt = "Select files for background sustraction"
initialdir = self.main.recWidget.folderEdit.text()
filenames = utils.getFilenames(txt, types=[], initialdir=initialdir)
print(
time.strftime("%Y-%m-%d %H:%M:%S") +
' Background subtraction started')
for filename in filenames:
print(
time.strftime("%Y-%m-%d %H:%M:%S") + ' Processing stack ' +
os.path.split(filename)[1])
ext = os.path.splitext(filename)[1]
filename2 = utils.insertSuffix(filename, '_subtracted')
if ext == '.hdf5':
with hdf.File(filename, 'r') as f0, \
hdf.File(filename2, 'w') as f1:
self.data = f0['data'].value
if len(self.data) > self.window:
dataSub = self.mpSubtract()
f1.create_dataset(name='data', data=dataSub)
else:
print('Stack shorter than filter window --> ignore')
elif ext in ['.tiff', '.tif']:
with tiff.TiffFile(filename) as tt:
self.data = tt.asarray()
if len(self.data) > self.window:
dataSub = self.mpSubtract()
tiff.imsave(filename2, dataSub)
else:
print('Stack shorter than filter window --> ignore')
print(
time.strftime("%Y-%m-%d %H:%M:%S") +
' Background subtraction finished')
self.finished.emit()
def run(self):
txt = "Select files for background sustraction"
initialdir = self.main.recWidget.folderEdit.text()
filenames = utils.getFilenames(txt, types=[], initialdir=initialdir)
print(time.strftime("%Y-%m-%d %H:%M:%S") +
' Background subtraction started')
for filename in filenames:
print(time.strftime("%Y-%m-%d %H:%M:%S") +
' Processing stack ' + os.path.split(filename)[1])
ext = os.path.splitext(filename)[1]
filename2 = utils.insertSuffix(filename, '_subtracted')
if ext == '.hdf5':
with hdf.File(filename, 'r') as f0, \
hdf.File(filename2, 'w') as f1:
self.data = f0['data'].value
if len(self.data) > self.window:
dataSub = self.mpSubtract()
f1.create_dataset(name='data', data=dataSub)
else:
print('Stack shorter than filter window --> ignore')
elif ext in ['.tiff', '.tif']:
with tiff.TiffFile(filename) as tt:
self.data = tt.asarray()
if len(self.data) > self.window:
dataSub = self.mpSubtract()
tiff.imsave(filename2, dataSub)
else:
print('Stack shorter than filter window --> ignore')
print(time.strftime("%Y-%m-%d %H:%M:%S") +
' Background subtraction finished')
self.finished.emit()