AdaptiveMotorControlLab/CellSeg3D

no display ?

Nal44 opened this issue · 4 comments

Nal44 commented

Hi,

I installed the plugin and I have no issues so far, the models runs , but I have no display in Napari ?
Is it suppose to provide the a new label layer in order to visualize the results and adjust parameters ?

Thanks,
antho

Nal44 commented

once done I get no display and:
my images are Tif 8bits ... (Z,X,Y)

any ideas ?
thanks
antho

"During handling of the above exception, another exception occurred:

Traceback (most recent call last):
File "C:\Users\m197816\AppData\Roaming\Python\Python310\site-packages\napari_cellseg3d\code_models\worker_inference.py", line 957, in inference
inference_loader = self.load_folder()
File "C:\Users\m197816\AppData\Roaming\Python\Python310\site-packages\napari_cellseg3d\code_models\worker_inference.py", line 212, in load_folder
data_check = LoadImaged(keys=["image"], image_only=True)(
File "C:\Users\m197816\AppData\Roaming\Python\Python310\site-packages\monai\transforms\io\dictionary.py", line 162, in call
data = self.loader(d[key], reader)
File "C:\Users\m197816\AppData\Roaming\Python\Python310\site-packages\monai\transforms\io\array.py", line 255, in call
img = reader.read(filename)
File "C:\Users\m197816\AppData\Roaming\Python\Python310\site-packages\monai\data\image_reader.py", line 258, in read
img.append(itk.imread(name, **kwargs_))
File "C:\Users\m197816\AppData\Roaming\Python\Python310\site-packages\itk\support\extras.py", line 1313, in imread
reader = template_reader_type.New(**kwargs)
File "C:\Users\m197816\AppData\Roaming\Python\Python310\site-packages\itk\support\template_class.py", line 661, in New
return self._NewImageReader(
File "C:\Users\m197816\AppData\Roaming\Python\Python310\site-packages\itk\support\template_class.py", line 191, in _NewImageReader
ImageType = itk.Image[PixelType, dimension]
File "C:\Users\m197816\AppData\Roaming\Python\Python310\site-packages\itk\support\template_class.py", line 529, in getitem
raise itk.TemplateTypeError(self, key)
itk.support.extras.TemplateTypeError: itk.Image is not wrapped for input type itk.RGBPixel[itk.US], int.

To limit the size of the package, only a limited number of
types are available in ITK Python. To print the supported
types, run the following command in your python environment:

itk.Image.GetTypes()

Possible solutions:

  • If you are an application user:
    ** Convert your input image into a supported format (see below).
    ** Contact developer to report the issue.

  • If you are an application developer, force input images to be
    loaded in a supported pixel type.

    e.g.: instance = itk.Image[itk.RGBPixel[itk.UC], int].New(my_input)

  • (Advanced) If you are an application developer, build ITK Python yourself and
    turned to ON the corresponding CMake option to wrap the pixel type or image
    dimension you need. When configuring ITK with CMake, you can set
    ITK_WRAP_${type} (replace ${type} with appropriate pixel type such as
    double). If you need to support images with 4 or 5 dimensions, you can add
    these dimensions to the list of dimensions in the CMake variable
    ITK_WRAP_IMAGE_DIMS.

Supported input types:

itk.RGBPixel[itk.UC]
itk.RGBAPixel[itk.UC]
itk.Vector[itk.F,2]
itk.Vector[itk.F,3]
itk.Vector[itk.F,4]
itk.CovariantVector[itk.F,2]
itk.CovariantVector[itk.F,3]
itk.CovariantVector[itk.F,4]
itk.SS
itk.UC
itk.US
itk.F
itk.D
itk.complex[itk.D]
itk.complex[itk.F]
itk.Vector[itk.D,2]
itk.Vector[itk.D,3]
itk.Vector[itk.D,4]
itk.SI
itk.UI
itk.UL
itk.ULL
itk.B
itk.FixedArray[itk.F,2]
itk.FixedArray[itk.D,2]
itk.Offset[2]
itk.SymmetricSecondRankTensor[itk.D,2]
itk.SymmetricSecondRankTensor[itk.F,2]
itk.RGBPixel[itk.UC]
itk.RGBAPixel[itk.UC]
itk.Vector[itk.F,2]
itk.Vector[itk.F,3]
itk.Vector[itk.F,4]
itk.CovariantVector[itk.F,2]
itk.CovariantVector[itk.F,3]
itk.CovariantVector[itk.F,4]
itk.SS
itk.UC
itk.US
itk.F
itk.D
itk.complex[itk.D]
itk.complex[itk.F]
itk.Vector[itk.D,2]
itk.Vector[itk.D,3]
itk.Vector[itk.D,4]
itk.SI
itk.UI
itk.UL
itk.ULL
itk.B
itk.FixedArray[itk.F,3]
itk.FixedArray[itk.D,3]
itk.Offset[3]
itk.SymmetricSecondRankTensor[itk.D,3]
itk.SymmetricSecondRankTensor[itk.F,3]
itk.RGBPixel[itk.UC]
itk.RGBAPixel[itk.UC]
itk.Vector[itk.F,2]
itk.Vector[itk.F,3]
itk.Vector[itk.F,4]
itk.CovariantVector[itk.F,2]
itk.CovariantVector[itk.F,3]
itk.CovariantVector[itk.F,4]
itk.SS
itk.UC
itk.US
itk.F
itk.D
itk.complex[itk.D]
itk.complex[itk.F]
itk.Vector[itk.D,2]
itk.Vector[itk.D,3]
itk.Vector[itk.D,4]
itk.SI
itk.UI
itk.UL
itk.ULL
itk.B
itk.FixedArray[itk.F,4]
itk.FixedArray[itk.D,4]
itk.Offset[4]
itk.SymmetricSecondRankTensor[itk.D,4]
itk.SymmetricSecondRankTensor[itk.F,4]
itk.Vector[itk.F,1]
itk.Vector[itk.F,1]
itk.Vector[itk.D,2]
itk.Vector[itk.D,3]
itk.Vector[itk.D,4]
itk.Vector[itk.F,1]
itk.CovariantVector[itk.D,2]
itk.CovariantVector[itk.D,3]
itk.CovariantVector[itk.D,4]
itk.CovariantVector[itk.D,2]
itk.CovariantVector[itk.D,3]
itk.CovariantVector[itk.D,4]
itk.CovariantVector[itk.D,2]
itk.CovariantVector[itk.D,3]
itk.CovariantVector[itk.D,4]
itk.NormalBandNode[itk.Image[itk.F,2]]
itk.NormalBandNode[itk.Image[itk.D,2]]
itk.NormalBandNode[itk.Image[itk.F,3]]
itk.NormalBandNode[itk.Image[itk.D,3]]
itk.NormalBandNode[itk.Image[itk.F,4]]
itk.NormalBandNode[itk.Image[itk.D,4]]

10:57:35 INFO
Worker finished at 10:57:35
10:57:35 INFO ********************
"

Nal44 commented

converting the tif file to a numpy array made the trick.
Runnning now :)

C-Achard commented

Hello Anthony,

Thanks for opening an issue, and sorry you ran into this problem.

Since the initial problem has been fixed, I will close this issue for now, but please feel free to reopen it or create a new one if you encounter any other problem.

Also happy to help with training models or if you have any other questions; please let me know.
Hope the models work well for you !

Best,
Cyril

Nal44 commented

thanks , yes training is next on my list, the pre-trained don't give good results on my images, but I really like the facts that many architectures are available :) , thanks !
antho