def _Run(self, parent, params, comm_title):
input_files = m.ObtainImageFiles(params['Image Folder'])
if len(input_files) == 0:
print('No images in the Image Folder.')
return False
im = m.imread(input_files[0], cv2.IMREAD_UNCHANGED)
root, ext_image = os.path.splitext(os.path.basename(input_files[0]))
print('')
print('Target file to check color type : ', input_files[0])
print('Image dimensions : ', im.shape)
print('Image filetype : ', im.dtype)
image_size_x = im.shape[1]
image_size_y = im.shape[0]
if (image_size_x <= 256 or image_size_y <= 256):
print('Image size is too small.')
return False
# Generate tmpdir
tmpdir_standardized = os.path.join(
params['Output Segmentation Folder (Empty)'],
"standardized" + str(threading.get_ident()).zfill(6)[-6:])
if os.path.exists(tmpdir_standardized):
shutil.rmtree(tmpdir_standardized)
os.mkdir(tmpdir_standardized)
#
tmpdir_output = os.path.join(
params['Output Segmentation Folder (Empty)'],
"output" + str(threading.get_ident()).zfill(6)[-6:])
if os.path.exists(tmpdir_output):
shutil.rmtree(tmpdir_output)
os.mkdir(tmpdir_output)
## Check image size
max_image_size = params['Maximal unit image size']
if max_image_size == '512':
std_sizes = np.array([512])
elif max_image_size == '1024':
std_sizes = np.array([512, 1024])
elif max_image_size == '2048':
std_sizes = np.array([512, 1024, 2048])
else:
print('Internal error at Maximal unit image size.')
return False
max_std_size = np.max(std_sizes)
if image_size_x > max_std_size:
unit_image_size_x = max_std_size
num_tiles_x = np.int(np.ceil(float(image_size_x) / max_std_size))
else:
unit_image_size_x = np.min(std_sizes[std_sizes >= image_size_x])
num_tiles_x = 1
if image_size_y > max_std_size:
unit_image_size_y = max_std_size
num_tiles_y = np.int(np.ceil(float(image_size_y) / max_std_size))
else:
unit_image_size_y = np.min(std_sizes[std_sizes >= image_size_y])
num_tiles_y = 1
#
converted_size_x = unit_image_size_x * num_tiles_x
converted_size_y = unit_image_size_y * num_tiles_y
fringe_size_x = converted_size_x - image_size_x
fringe_size_y = converted_size_y - image_size_y
#
#
output_files = []
print('Image standardization: ')
for input_file in input_files:
im_col = m.imread(input_file)
# im_col = self._ChangeIntoColor(im_col)
filename = path.basename(input_file)
print(filename + ' ')
for ext in [
'.TIF', '.tif', '.TIFF', '.tiff', '.PNG', '.jpg', '.jpeg',
'.JPG', '.JPEG'
]:
filename = filename.replace(ext, '.png')
output_files.append(filename)
# add fringe X
im_fringe_x = cv2.flip(im_col, 1) # flipcode > 0, left-right
im_fringe_x = im_fringe_x[:, 0:fringe_size_x]
converted_image = cv2.hconcat([im_col, im_fringe_x])
# add fringe Y
im_fringe_y = cv2.flip(converted_image,
0) # flipcode = 0, top-bottom
im_fringe_y = im_fringe_y[0:fringe_size_y, :]
converted_image = cv2.vconcat([converted_image, im_fringe_y])
# Save
if (num_tiles_x == 1) and (num_tiles_y == 1):
converted_filename = os.path.join(tmpdir_standardized,
filename)
m.imwrite(converted_filename, converted_image)
else:
for iy in range(num_tiles_y):
for ix in range(num_tiles_x):
y0 = iy * unit_image_size_y
y1 = y0 + unit_image_size_y
x0 = ix * unit_image_size_x
x1 = x0 + unit_image_size_x
current_tile = converted_image[y0:y1, x0:x1]
converted_filename = str(ix).zfill(3)[-3:] + '_' + str(
iy).zfill(3)[-3:] + '_' + filename
converted_filename = os.path.join(
tmpdir_standardized, converted_filename)
m.imwrite(converted_filename, current_tile)
#Complete
print('')
print('Images were split and changed into RGB 8bit, and stored in ',
tmpdir_standardized)
print('')
tmp = ['--mode' , 'predict' , \
'--save_freq' , '0' , \
'--input_dir' , tmpdir_standardized, \
'--output_dir' , tmpdir_output, \
'--checkpoint' , params['Model Folder'], \
'--image_height', str(unit_image_size_y), \
'--image_width' , str(unit_image_size_x)]
comm = parent.u_info.exec_translate[:]
comm.extend(tmp)
print('')
print(' '.join(comm))
print('')
print('Start inference.')
print('')
m.UnlockFolder(parent.u_info,
params['Output Segmentation Folder (Empty)']
) # Only for shared folder/file
s.run(comm)
print('')
print('Segmentation reconstruction: ')
for output_file in output_files:
##
if (num_tiles_x == 1) and (num_tiles_y == 1):
## Remove fringes
filename = os.path.join(tmpdir_output, output_file)
inferred_segmentation = m.imread(filename,
flags=cv2.IMREAD_GRAYSCALE,
dtype='uint8')
else:
## Merge split images.
inferred_segmentation = np.zeros(
(converted_size_y, converted_size_x), dtype='uint8')
for iy in range(num_tiles_y):
for ix in range(num_tiles_x):
y0 = iy * unit_image_size_y
y1 = y0 + unit_image_size_y
x0 = ix * unit_image_size_x
x1 = x0 + unit_image_size_x
current_tile_filename = str(ix).zfill(
3)[-3:] + '_' + str(iy).zfill(
3)[-3:] + '_' + output_file
current_tile_filename = os.path.join(
tmpdir_output, current_tile_filename)
current_tile = m.imread(current_tile_filename,
flags=cv2.IMREAD_GRAYSCALE,
dtype='uint8')
inferred_segmentation[y0:y1,
x0:x1] = current_tile[:, :]
inferred_segmentation = inferred_segmentation[0:image_size_y,
0:image_size_x]
print('inferred_segmentation: ', inferred_segmentation.shape,
inferred_segmentation.dtype)
## Save
filename_base = os.path.splitext(os.path.basename(output_file))[0]
filename_base = os.path.join(
params['Output Segmentation Folder (Empty)'], filename_base)
filetype = params['Output Filetype']
if filetype == '8-bit gray scale PNG':
filename = filename_base + '.png'
m.save_png8(inferred_segmentation, filename)
elif filetype == '8-bit gray scale TIFF (Uncompressed)':
filename = filename_base + '.tif'
m.save_tif8(inferred_segmentation, filename, compression=1)
elif filetype == '8-bit gray scale TIFF (Compressed)':
filename = filename_base + '.tif'
m.save_tif8(inferred_segmentation, filename)
else:
print('Internel error: bad filetype.')
print(filename)
##
# rm tmpdir
if os.path.exists(tmpdir_standardized):
shutil.rmtree(tmpdir_standardized)
if os.path.exists(tmpdir_output):
shutil.rmtree(tmpdir_output)
parent.parent.ExecuteCloseFileFolder(
params['Output Segmentation Folder (Empty)'])
parent.parent.OpenFolder(params['Output Segmentation Folder (Empty)'])
print('')
print('Finish inference.')
print('')
return True
def _Run(self, parent, params, comm_title):
##
## Transform bitdepth of EM images and segmentation in the target directory.
## Translate.py only accepts unit24 (RGB color).
##
img_files = glob.glob(os.path.join(params['Image Folder'], "*.jpg"))
img_png = glob.glob(os.path.join(params['Image Folder'], "*.png"))
img_tif = glob.glob(os.path.join(params['Image Folder'], "*.tif"))
img_files.extend(img_png)
img_files.extend(img_tif)
img_files = sorted(img_files)
if len(img_files) == 0:
print('No image file.')
return False
im = m.imread(img_files[0], cv2.IMREAD_UNCHANGED)
print('')
print('Number of images : ', len(img_files))
print('Image color type : ', img_files[0])
print('Image dimensions : ', im.shape)
print('Image filetype : ', im.dtype)
seg_files = glob.glob(
os.path.join(params['Segmentation Folder'], "*.jpg"))
seg_png = glob.glob(
os.path.join(params['Segmentation Folder'], "*.png"))
seg_tif = glob.glob(
os.path.join(params['Segmentation Folder'], "*.tif"))
seg_files.extend(seg_png)
seg_files.extend(seg_tif)
seg_files = sorted(seg_files)
if len(seg_files) == 0:
print('')
print('No segmentation file.')
print('Aborted.')
return False
sg = m.imread(seg_files[0], cv2.IMREAD_UNCHANGED)
print('')
print('Number of Segmentation images : ', len(seg_files))
print('Segmentation image dimensions : ', sg.shape)
print('Segmentation filetype : ', sg.dtype)
print('')
if len(img_files) != len(seg_files):
print(
'The number of images is not equal to that of segmenation images.'
)
print('Aborted.')
return False
# Generate tmpdir
tmpdir = os.path.join(params['Model Folder (Empty)'], "paired" +
str(threading.get_ident()).zfill(6)[-6:]) # )
if os.path.exists(tmpdir):
shutil.rmtree(tmpdir)
os.mkdir(tmpdir)
for img_file, seg_file in zip(img_files, seg_files):
img = m.imread(img_file)
seg = m.imread(seg_file)
img = np.array(img, dtype=np.uint8)
seg = np.array(seg, dtype=np.uint8)
if len(img.shape) == 2:
img = cv2.cvtColor(img, cv2.COLOR_GRAY2BGR)
elif img.shape[2] == 4:
img = cv2.cvtColor(img, cv2.COLOR_BGRA2BGR)
elif img.shape[2] != 3:
print('File is broken: ', img_file)
print('Aborted.')
return False
if len(seg.shape) == 2:
seg = cv2.cvtColor(seg, cv2.COLOR_GRAY2BGR)
elif seg.shape[2] == 4:
seg = cv2.cvtColor(seg, cv2.COLOR_BGRA2BGR)
elif seg.shape[2] != 3:
print('File is broken: ', seg_file)
print('Aborted.')
return False
paired = cv2.hconcat([img, seg])
tmpname = os.path.splitext(os.path.basename(img_file))[0]
filename_paired = os.path.join(tmpdir, tmpname + '.png')
m.imwrite(filename_paired, paired)
print('Paired images (RGB 8bit) are stored in ', tmpdir)
print('')
#
# Dialog to specify directory
#
aug = params['Augmentation']
if aug == "fliplr, flipud, transpose":
augmentation = ['--fliplr', '--flipud', '--transpose']
elif aug == "fliplr, flipud":
augmentation = ['--fliplr', '--flipud', '--no_transpose']
elif aug == "fliplr":
augmentation = ['--fliplr', '--no_flipud', '--no_transpose']
elif aug == "flipud":
augmentation = ['--no_fliplr', '--flipud', '--no_transpose']
elif aug == "None":
augmentation = ['--no_fliplr', '--no_flipud', '--no_transpose']
else:
print(
"Internal error at Augumentation of PartDialogTrainingExecutor."
)
self._Cancel()
return False
#
# ' --model ' + params['Model'] + ' '
#
# parent.u_info.exec_translate, \
tmp = ['--batch_size' , '4', \
'--mode' , 'train', \
'--input_dir' , tmpdir, \
'--output_dir' , params['Model Folder (Empty)'], \
'--loss' , params['Loss Function'], \
'--network' , params['Network'], \
'--max_epochs' , str( params['Maximal Epochs'] ), \
'--display_freq' , str( params['Display Frequency'] ), \
'--u_depth' , str( params['U depth'] ), \
'--n_res_blocks' , str( params['N res blocks'] ), \
'--n_highway_units', str( params['N highway units'] ), \
'--n_dense_blocks' , str( params['N dense blocks'] ), \
'--n_dense_layers' , str( params['N dense layers']) ]
comm = parent.u_info.exec_translate[:]
comm.extend(tmp)
comm.extend(augmentation)
print('')
print(' '.join(comm))
print('')
print('Start training.')
print('')
m.UnlockFolder(parent.u_info, params['Model Folder (Empty)'])
s.run(comm)
# rm tmpdir
if os.path.exists(tmpdir):
shutil.rmtree(tmpdir)
## m.LockFolder(parent.u_info, params['Model Folder (Empty)']) ## Tentatively commented out.
parent.parent.ExecuteCloseFileFolder(params['Model Folder (Empty)'])
parent.parent.OpenFolder(params['Model Folder (Empty)'])
print('')
print('Finish training.')
print('')
return True
