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 tiff2png(main, filenames=None):
if filenames is None:
filenames = utils.getFilenames('Load TIFF files',
[('Tiff files', '.tiff'),
('Tif files', '.tif')],
main.recWidget.folderEdit.text())
for filename in filenames:
with tiff.TiffFile(filename) as tt:
arr = tt.asarray()
cmin, cmax = bestLimits(arr)
arr[arr > cmax] = cmax
arr[arr < cmin] = cmin
arr -= arr.min()
arr = arr/arr.max()
arr = imresize(arr, (1000, 1000), 'nearest')
im = Image.fromarray(cm.cubehelix(arr, bytes=True))
im.save(os.path.splitext(filename)[0] + '.png')
def tiff2png(main, filenames=None):
if filenames is None:
filenames = utils.getFilenames('Load TIFF files',
[('Tiff files', '.tiff'),
('Tif files', '.tif')],
main.recWidget.folderEdit.text())
for filename in filenames:
with tiff.TiffFile(filename) as tt:
arr = tt.asarray()
cmin, cmax = bestLimits(arr)
arr[arr > cmax] = cmax
arr[arr < cmin] = cmin
arr -= arr.min()
arr = arr / arr.max()
arr = imresize(arr, (1000, 1000), 'nearest')
im = Image.fromarray(cm.cubehelix(arr, bytes=True))
im.save(os.path.splitext(filename)[0] + '.png')
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()