def onSaveImage(self):
'''called when Save Image is pressed'''
reImg = self.ui.mImageDisplay.data
if reImg is None:
QtGui.QMessageBox.critical\
(self, self.tr('Error'),\
self.tr('Nothing reconstructed.'))
return
filterStr = 'Images (*.tiff *.h5)'
if self.opts['recon']['out_format'] == 'hdf5':
filterStr = 'Images (*.h5)'
elif self.opts['recon']['out_format'] == 'tiff':
filterStr = 'Images (*.tiff)'
filename = QtGui.QFileDialog.getSaveFileName\
(self, 'Save Image',\
self.opts['extra']['dest_dir'], filterStr)
filename = str(filename)
basename, extname = splitext(filename)
if extname == '.tiff':
self.logText('Saving image data to ' + filename + '\n')
imageList = [reImg[:,:,i] for i in range(reImg.shape[2])]
fi.write_multipage(imageList, filename)
elif extname == '.h5':
self.logText('Saving image data to ' + filename)
f = h5py.File(filename, 'w')
f['reImg'] = reImg
f.close()
else:
QtGui.QMessageBox.critical\
(self.tr('Output format ' + extname[1:] +\
' not supported'))
self.logText('Done\n')
def test_write_multipage():
shape = (64, 64, 64)
x = np.ones(shape, dtype=np.uint8) * np.random.rand(*shape) * 255
x = x.astype(np.uint8)
f = NamedTemporaryFile(suffix='.tif')
fname = f.name
f.close()
fi.write_multipage(x, fname)
y = fi.read_multipage(fname)
assert_array_equal(x, y)
def test_write_multipage():
shape = (64, 64, 64)
x = np.ones(shape, dtype=np.uint8) * np.random.random(shape) * 255
x = x.astype(np.uint8)
f = NamedTemporaryFile(suffix='.tif')
fname = f.name
f.close()
fi.write_multipage(x, fname)
y = fi.read_multipage(fname)
assert_array_equal(x, y)
def writeFullFramesTiff(masked_image_file, tiff_file = -1, reduce_fractor = 8, base_name = '', status_queue = ''):
'''
write scale down the saved full frames, and put them into a tiff stack.
requires either install skimage with the freeimage library plugin, or the tifffile module.
'''
#if no tiff_file is given, the save name will be derived from masked_image_file
if tiff_file == -1:
tiff_file = os.path.splitext(masked_image_file)[0] + '_full.tiff';
mask_fid = h5py.File(masked_image_file, "r");
#determine the expected size of the full_data size with respect to the
#number of frames in full_data and the same interval (I only do that
#to correct for a bug in previously saved files)
expected_size = int(np.floor(mask_fid["/mask"].shape[0]/float(mask_fid["/full_data"].attrs['save_interval']) + 1));
if expected_size > mask_fid["/full_data"].shape[0]:
expected_size = mask_fid["/full_data"].shape[0]
#initialized reduced array
im_size = tuple(np.array(mask_fid["/full_data"].shape)[1:]/reduce_fractor)
reduce_factor = (im_size[-1], im_size[-2])
I_worms = np.zeros((expected_size, im_size[0],im_size[1]), dtype = np.uint8)
sendQueueOrPrint(status_queue, 'Reading for data the tiff file...', base_name);
for frame_number in range(expected_size):
I_worms[frame_number, :,:] = cv2.resize(mask_fid["/full_data"][frame_number,:,:], reduce_factor);
sendQueueOrPrint(status_queue, 'Writing tiff file...', base_name);
try:
#Requires the installation of freeimage library.
#On mac is trivial using brew (brew install freeimage),
#but i am not sure how to do it on windows
from skimage.io._plugins import freeimage_plugin as fi
fi.write_multipage(I_worms, tiff_file, fi.IO_FLAGS.TIFF_LZW) #the best way I found to write lzw compression on python
except:
import tifffile #pip intall tifffile
#For some reason gzip compression appears as an inverted image in
#preview (both windows and mac), but it is read correctly in ImageJ
tifffile.imsave(tiff_file, I_worms, compress=4)
sendQueueOrPrint(status_queue, 'Tiff file done.', base_name);
elif not os.path.isdir(bmpDir):
os.mkdir(bmpDir)
chunk = 56
frameIni = 16449
NImages = 450
I = np.zeros((NImages, 2048, 2048), dtype=np.uint8)
for nn in range(NImages):
filename = '/Users/ajaver/Desktop/DCR_D_56/DCR_D_%i_%i.BMP' % (chunk, nn +
frameIni)
I[nn, :, :] = smisc.imread(filename)[:, :, 0] #change rgb to gray
#plt.figure()
#plt.imshow(I[:,:,nn])
fi.write_multipage(I, saveDir + 'Tiff_LZW.tiff', fi.IO_FLAGS.TIFF_LZW)
fi.write_multipage(I, saveDir + 'Tiff_Uncompressed.tiff',
fi.IO_FLAGS.TIFF_NONE)
for nn in range(I.shape[0]):
fi.write(I[nn, :, :], bmpDir + '%03i.bmp' % nn)
# Change John's BMP into index-value arrays
FID = open(saveDir + 'reduced_indexes', "wb")
# Find list of indexes and pixel values
for nn in range(I.shape[0]):
Isingle = I[nn, :, :]
mask = (Isingle != 200) & (Isingle != 0)
indexList = np.where(mask)
# else: # for frame in range(expected_size): # I_worms[frame, :,:] = cv2.resize(mask_fid["/full_data"][frame,:,:], im_size); # # # fi.write_multipage(I_worms, tiff_file, fi.IO_FLAGS.TIFF_LZW) root_dir = '/Users/ajaver/Downloads/wetransfer-2af646/' #'/Volumes/ajaver$/GeckoVideo/Compressed/' base_file = 'CaptureTest_90pc_Ch3_21022015_205929' masked_image_file = root_dir + base_file + '.hdf5' tiff_file = root_dir + base_file + '_mask_deflate.tiff' mask_fid = h5py.File(masked_image_file, "r") fi.write_multipage(mask_fid["/mask"], tiff_file, fi.IO_FLAGS.TIFF_DEFLATE) #masked_image_file = rootDir + 'Capture_Ch3_26022015_161436.hdf5' #masked_image_file = '/Volumes/behavgenom$/GeckoVideo/Compressed/20150218/CaptureTest_90pc_Ch2_18022015_230213.hdf5' #root_dir = '/Volumes/behavgenom$/GeckoVideo/Compressed/20150218/'; #base_file = 'CaptureTest_90pc_Ch%i_18022015_230213' #root_dir = '/Volumes/behavgenom$/GeckoVideo/Compressed/20150216/'; #base_file = 'CaptureTest_90pc_Ch%i_16022015_174636' #root_dir = '/Volumes/ajaver$/GeckoVideo/Compressed/' #base_file = 'CaptureTest_90pc_Ch1%i_20022015_183607' # #for ch_ind in range(1,2): # channel_file = (base_file % ch_ind) # masked_image_file = root_dir + channel_file + '.hdf5'
# for frame in range(expected_size):
# I_worms[frame, :,:] = cv2.resize(mask_fid["/full_data"][frame,:,:], im_size);
#
#
# fi.write_multipage(I_worms, tiff_file, fi.IO_FLAGS.TIFF_LZW)
root_dir = '/Users/ajaver/Downloads/wetransfer-2af646/' #'/Volumes/ajaver$/GeckoVideo/Compressed/'
base_file = 'CaptureTest_90pc_Ch3_21022015_205929'
masked_image_file = root_dir + base_file + '.hdf5'
tiff_file = root_dir + base_file + '_mask_deflate.tiff'
mask_fid = h5py.File(masked_image_file, "r");
fi.write_multipage(mask_fid["/mask"], tiff_file, fi.IO_FLAGS.TIFF_DEFLATE)
#masked_image_file = rootDir + 'Capture_Ch3_26022015_161436.hdf5'
#masked_image_file = '/Volumes/behavgenom$/GeckoVideo/Compressed/20150218/CaptureTest_90pc_Ch2_18022015_230213.hdf5'
#root_dir = '/Volumes/behavgenom$/GeckoVideo/Compressed/20150218/';
#base_file = 'CaptureTest_90pc_Ch%i_18022015_230213'
#root_dir = '/Volumes/behavgenom$/GeckoVideo/Compressed/20150216/';
#base_file = 'CaptureTest_90pc_Ch%i_16022015_174636'
#root_dir = '/Volumes/ajaver$/GeckoVideo/Compressed/'
#base_file = 'CaptureTest_90pc_Ch1%i_20022015_183607'
#
#for ch_ind in range(1,2):
# channel_file = (base_file % ch_ind)
def saveTiff3d(filepath, img):
nx, ny, nz = img.shape
imglist = [img[:, :, idx] for idx in xrange(nz)]
fi.write_multipage(imglist, filepath)
if ma > norm[channel]['Max']:
norm[channel]['Max'] = ma
if options.min:
norm[channel]['Min'] = options.min[c]
else:
mi = np.min(im)
if mi > norm[channel]['Min']:
norm[channel]['Min'] = mi
else:
norm[channel]['Max'] = options.max[c]
norm[channel]['Min'] = options.min[c]
print("Normalization values: {}".format(norm))
print("Extracting ...")
for c in range(len(channels)):
print("Extracting channel: {}".format(channels[c]))
channel = channels[c]
for timepoint in timepoints:
print("Extracting timepoint: {}".format(timepoint))
im = hdf5.get('t{0:05d}/{1}/{2}/cells'.format(timepoint, channel, L)).value.astype(np.int16)
if options.crop:
c = int(options.crop)
im = im[c:-c, c:-c, c:-c]
if options.normalize:
im = rescale(im, Min=norm[channel]['Min'], Max=norm[channel]['Max'])
freeimg.write_multipage(im, outfiles[c] + '_{}_{}.tiff'.format(timepoint, L))
print("Cube Dimensions: | x {} | y {} | z {} |".format(im.shape[0], im.shape[1], im.shape[2]))