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Workflow channel fix and cropping fix #23

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merged 3 commits into from
Oct 27, 2023
Merged

Workflow channel fix and cropping fix #23

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abb67fa
fix workflow channel saving incompatabilities
TimMonko Apr 26, 2023
cac56ba
solve not cropping in utilities widget
TimMonko Apr 27, 2023
0ab0a66
Merge branch 'main' into workflow-channel-fix
TimMonko Oct 27, 2023
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29 changes: 26 additions & 3 deletions src/napari_ndev/_widget.py
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Original file line number Diff line number Diff line change
Expand Up @@ -121,6 +121,16 @@ def batch_utilities(

image_list = os.listdir(image_directory)

img = AICSImage(image_directory / image_list[0])

all_x, all_y, all_z = False, False, False
if X_range == slice(0, img.dims.X, 1):
all_x = True
if Y_range == slice(0, img.dims.Y, 1):
all_y = True
if Z_range == slice(0, img.dims.Z, 1):
all_z = True

for file in tqdm(image_list, label="file"):
result_stack = None
img = AICSImage(image_directory / file)
Expand Down Expand Up @@ -148,6 +158,13 @@ def batch_utilities(
)

# T C Z Y X default from aicsimageio
if all_x is True:
X_range = slice(0, img.dims.X, 1)
if all_y is True:
Y_range = slice(0, img.dims.Y, 1)
if all_z is True:
Z_range = slice(0, img.dims.Z, 1)

ch_img = ch_img[:, :, Z_range, Y_range, X_range]

# project along the Z axis (2)
Expand Down Expand Up @@ -380,17 +397,21 @@ def batch_workflow(
image_stack = []
img = AICSImage(image_directory / file)

"""for each root selected in the root list, extract the channel image
and set the workflow root names, this will be used later for workflow.get
"""
for idx, root in enumerate(root_list):
ch_img = _get_channel_image(img=img, dims=img_dims, channel=root)

ch_img = _get_channel_image(
img=img, dims=img_dims, channel=root)
print(ch_img.shape)
wf.set(name=wf.roots()[idx], func_or_data=ch_img)

image_stack.append(ch_img)

# dask_stack = da.stack(image_stack, axis=0)

result = wf.get(name=wf.leafs())
result_stack = cle.pull(result)
result_stack = cle.pull(result) # adds a new dim at 0th axis, as "C"

"""extract the leaf name corresponding to each root to save into
channel names
Expand All @@ -407,6 +428,8 @@ def batch_workflow(
result_stack = da.concatenate([dask_images, dask_result], axis=0)
result_names = root_list + result_names

# print(result_stack.shape)

save_name = str(file + ".ome.tif")
save_uri = result_directory / save_name

Expand Down
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