def test_mosaic_image_two(data_dir, fname, expects):
with open(data_dir / fname, 'rb') as fp:
czi = CziFile(czi_filename=fp)
sze = czi.read_mosaic_size()
rgion = (sze[0], sze[1], int(sze[2] / 2), int(sze[3] / 2))
img = czi.read_mosaic(region=rgion, C=0, M=0)
assert img.shape == expects
def test_mosaic_image(data_dir, fname, expects):
with open(data_dir / fname, 'rb') as fp:
czi = CziFile(czi_filename=fp)
sze = czi.read_mosaic_size()
assert sze[2] == 1756
assert sze[3] == 624
img = czi.read_mosaic(scale_factor=0.1, C=0)
assert img.shape[0] == 1
def __init__(self, slide_path: str):
self.slide_path = slide_path
reader = CziFile(slide_path)
if not reader.is_mosaic():
raise NotImplementedError(
'This class has only been defined for mosaic czi files. '
'You should be able to simply convert the non-mosaic czi-file '
'into a format that can be opened with openslide.'
)
self.bboxes = np.array(reader.mosaic_scene_bounding_boxes())
self.data_mask = self._get_data_mask(self.bboxes)
self.shape = reader.read_mosaic_size()
self.dimensions = self.shape[2:]
self.region_mask = self._get_region_mask(self.shape)
print('Using AICSImageIO to read the image.')
all_scenes_array = img.get_image_dask_data()
if not use_aicsimageio and use_pylibczi is True:
# read CZI using aicspylibczi
czi = CziFile(filename)
# for testing
# Get the shape of the data
print('Dimensions : ', czi.dims)
print('Size : ', czi.size)
print('Shape : ', czi.dims_shape())
print('IsMoasic : ', czi.is_mosaic())
if czi.is_mosaic():
print('Mosaic Size : ', czi.read_mosaic_size())
# get the required shape for all and single scenes
shape_all, shape_single, same_shape = czt.get_shape_allscenes(czi, md)
print('Required_Array Shape for all scenes: ', shape_all)
for sh in shape_single:
print('Required Array Shape for single scenes: ', sh)
#array_type = 'dask'
array_type = 'zarr'
#array_type = 'numpy'
if array_type == 'zarr':
# define array to store all channels
print('Using aicspylibCZI to read the image (ZARR array).')
def test_mosaic_size(data_dir, fname, expected):
czi = CziFile(str(data_dir / fname))
ans = czi.read_mosaic_size()
assert ans == expected
def open_image_stack(filepath):
""" Open a file using AICSImageIO and display it using napari
:param path: filepath of the image
:type path: str
"""
if os.path.isfile(filepath):
# remove existing layers from napari
viewer.layers.select_all()
viewer.layers.remove_selected()
# get the metadata
metadata, add_metadata = czt.get_metadata_czi(filepath)
# add the global metadata and adapt the table display
mdbrowser.update_metadata(metadata)
mdbrowser.update_style()
use_aicsimageio = True
use_pylibczi = False
# decide which tool to use to read the image
if metadata['ImageType'] != 'czi':
use_aicsimageio = True
elif metadata['ImageType'] == 'czi' and metadata['isMosaic'] is False:
use_aicsimageio = True
elif metadata['ImageType'] == 'czi' and metadata['isMosaic'] is True:
use_aicsimageio = False
use_pylibczi = True
"""
# check if CZI has T or Z dimension
hasT = False
hasZ = False
if 'T' in metadata['dims_aicspylibczi']:
hasT = True
if 'Z' in metadata['dims_aicspylibczi']:
hasZ = True
"""
if use_aicsimageio:
# get AICSImageIO object
img = AICSImage(filepath)
# check if the Dask Delayed Reader should be used
if not checkboxes.cbox_dask.isChecked():
print('Using AICSImageIO normal ImageReader.')
all_scenes_array = img.get_image_data()
if checkboxes.cbox_dask.isChecked():
print('Using AICSImageIO Dask Delayed ImageReader')
all_scenes_array = img.get_image_dask_data()
if not use_aicsimageio and use_pylibczi is True:
# read CZI using aicspylibczi
czi = CziFile(filepath)
# Get the shape of the data
print('Dimensions : ', czi.dims)
print('Size : ', czi.size)
print('Shape : ', czi.dims_shape())
print('IsMoasic : ', czi.is_mosaic())
if czi.is_mosaic():
print('Mosaic Size : ', czi.read_mosaic_size())
# get the required shape for all and single scenes
shape_all, shape_single, same_shape = czt.get_shape_allscenes(czi, metadata)
print('Required_Array Shape for all scenes: ', shape_all)
for sh in shape_single:
print('Required Array Shape for single scenes: ', sh)
if not same_shape:
print('No all scenes have the same shape. Exiting ...')
sys.exit()
#array_type = 'dask'
array_type = 'zarr'
#array_type = 'numpy'
if array_type == 'zarr':
# define array to store all channels
print('Using aicspylibCZI to read the image (ZARR array).')
# option 1
all_scenes_array = zarr.create(tuple(shape_all),
dtype=metadata['NumPy.dtype'],
chunks=True)
# option 2
# all_scenes_array = zarr.open(r'c:\Temp\czi_scene_all.zarr', mode='w',
# shape=shape_all,
# chunks=True,
# dtype=md['NumPy.dtype'])
if array_type == 'numpy':
print('Using aicspylibCZI to read the image (Numpy.Array).')
all_scenes_array = np.empty(shape_all, dtype=metadata['NumPy.dtype'])
if array_type == 'zarr' or array_type == 'numpy':
# loop over all scenes
for s in range(metadata['SizeS']):
# get the CZIscene for the current scene
single_scene = czt.CZIScene(czi, metadata, sceneindex=s)
out = czt.read_czi_scene(czi, single_scene, metadata)
all_scenes_array[s, :, :, :, :, :] = np.squeeze(out, axis=0)
print(all_scenes_array.shape)
elif array_type == 'dask':
def dask_load_sceneimage(czi, s, md):
# get the CZIscene for the current scene
single_scene = czt.CZIScene(czi, md, sceneindex=s)
out = czt.read_czi_scene(czi, single_scene, md)
return out
sp = shape_all[1:]
# create dask stack of lazy image readers
print('Using aicspylibCZI to read the image (Dask.Array) + Delayed Reading.')
lazy_process_image = dask.delayed(dask_load_sceneimage) # lazy reader
lazy_arrays = [lazy_process_image(czi, s, metadata) for s in range(metadata['SizeS'])]
dask_arrays = [
da.from_delayed(lazy_array, shape=sp, dtype=metadata['NumPy.dtype'])
for lazy_array in lazy_arrays
]
# Stack into one large dask.array
all_scenes_array = da.stack(dask_arrays, axis=0)
print(all_scenes_array.shape)
do_scaling = checkboxes.cbox_autoscale.isChecked()
# show the actual image stack
nap.show_napari(viewer, all_scenes_array, metadata,
blending='additive',
adjust_contrast=do_scaling,
gamma=0.85,
add_mdtable=False,
rename_sliders=True)
# filename = r"C:\Users\m1srh\OneDrive - Carl Zeiss AG\Testdata_Zeiss\CZI_Testfiles\Well_B2-4_S=4_T=1_Z=1_C=1.czi"
# filename = r"C:\Users\m1srh\OneDrive - Carl Zeiss AG\Testdata_Zeiss\CZI_Testfiles\W96_B2+B4_S=2_T=1=Z=1_C=1_Tile=5x9.czi"
# filename = r"C:\Users\m1srh\OneDrive - Carl Zeiss AG\Testdata_Zeiss\CZI_Testfiles\W96_B2+B4_S=2_T=2=Z=4_C=3_Tile=5x9.czi"
#filename = r"C:\Users\m1srh\OneDrive - Carl Zeiss AG\Testdata_Zeiss\Castor\Z-Stack_DCV\CellDivision_T=10_Z=15_CH=2_DCV_small.czi"
# filename = r"C:\Users\m1srh\OneDrive - Carl Zeiss AG\Testdata_Zeiss\Castor\Mouse Kidney_40x0.95_3CD_JK_comp.czi"
# filename = r"C:\Temp\input\DTScan_ID4.czi"
# filename = r"C:\Temp\input\OverViewScan_8Brains.czi"
#filename = r"C:\Users\m1srh\OneDrive - Carl Zeiss AG\Testdata_Zeiss\Castor\testwell96.czi"
filename = r"C:\Users\m1srh\OneDrive - Carl Zeiss AG\Testdata_Zeiss\CZI_Testfiles\Multiscene_CZI_3Scenes.czi"
# get the metadata from the czi file
md, additional_mdczi = imf.get_metadata(filename)
# read CZI using aicslibczi
cziobject = CziFile(filename)
size = cziobject.read_mosaic_size()
dimsizes = imf.getdims_pylibczi(cziobject)
print('Mosaic Size: ', size)
print('-----------------------------------------------------')
# define which scene to read
ch = 0
t = 0
z = 0
scalefactor = 1.0
#scenes2plot = 1
scenes2plot = md['SizeS']
"""
rs = strategies.RectangularStrategy()
# filename = r"/datadisk1/tuxedo/testpictures/Testdata_Zeiss/CZI_Testfiles/S=2_3x3_T=1_Z=1_CH=2.czi"
# filename = r"C:\Users\m1srh\OneDrive - Carl Zeiss AG\Testdata_Zeiss\CZI_Testfiles\S=2_3x3_T=1_Z=4_CH=2.czi"
# filename = r"C:\Users\m1srh\OneDrive - Carl Zeiss AG\Testdata_Zeiss\CZI_Testfiles\S=2_3x3_T=3_Z=1_CH=2.czi"
# filename = r"C:\Users\m1srh\OneDrive - Carl Zeiss AG\Testdata_Zeiss\CZI_Testfiles\S=1_3x3_T=3_Z=4_CH=2.czi"
# filename = r"C:\Users\m1srh\OneDrive - Carl Zeiss AG\Testdata_Zeiss\CZI_Testfiles\S=2_3x3_T=3_Z=4_CH=2.czi"
# filename = r"C:\Temp\input\DTScan_ID4_small.czi"
# filename = r"C:\Temp\input\OverViewScan_8Brains.czi"
# filename = r"C:\Users\m1srh\OneDrive - Carl Zeiss AG\Testdata_Zeiss\Castor\testwell96.czi"
# filename = r"C:\Users\m1srh\OneDrive - Carl Zeiss AG\Testdata_Zeiss\CZI_Testfiles\Multiscene_CZI_3Scenes.czi"
# get the metadata from the czi file
md, additional_mdczi = imf.get_metadata(filename)
# read CZI using aicslibczi
czi = CziFile(filename)
size = czi.read_mosaic_size()
# get all bboxes for all scenes from the CZI file
all_bboxes = czt.getbboxes_allscenes(czi, numscenes=md['SizeS'])
# read data for first scene
for s in all_bboxes:
scene_array = zarr.create(
(1, md['SizeT'], md['SizeZ'], md['SizeC'], s.height, s.width),
chunks=True)
# read a complete scene
for t, z, c in product(range(md['SizeT']), range(md['SizeZ']),
range(md['SizeC'])):
scene_slice, bbox, md = czt.read_scene_bbox(czi,
md,
