The dependency of tensorflow.keras

[TsungChihTsai]

I use the same method in the google colab

(your Tutorial: DeepD3 train your own neural network)

https://deepd3.forschung.fau.de/

I think it's the issue about the dependency. I attempted to install as follow:

!pip install deepd3
!pip install segmentation_models
!pip uninstall keras
!pip install keras==2.2.4
!pip install tensorflow-keras

However, it's still not work.

[anki-xyz]

I was just trying this now;
import tensorflow as tf
from tensorflow.keras.optimizers import Adam
just works fine for me on Colab... (also installing segmentation_models and deepd3 before)

[TsungChihTsai]

I tried the first two codes are workable. After I installed two modules of DeepD3 and segmentation_models, I still face the issue of segmentation_models. Get Outlook for iOS<https://aka.ms/o0ukef>

…

________________________________ From: anki-xyz ***@***.***> Sent: Wednesday, March 20, 2024 10:46:55 AM To: ankilab/DeepD3 ***@***.***> Cc: TsungChihTsai ***@***.***>; Author ***@***.***> Subject: Re: [ankilab/DeepD3] The dependency of tensorflow.keras (Issue #4) I was just trying this now; import tensorflow as tf from tensorflow.keras.optimizers import Adam just works fine for me on Colab... (also installing segmentation_models and deepd3 before) image.png (view on web)<https://github.com/ankilab/DeepD3/assets/11031615/cc56c9f3-0587-4f7f-9e2f-eaefa1ceec96> — Reply to this email directly, view it on GitHub<#4 (comment)>, or unsubscribe<https://github.com/notifications/unsubscribe-auth/A5PHX5NPBEQOTB4PATR7EV3YZGON7AVCNFSM6AAAAABCGDPGYSVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDAMBZG42DSNBYGU>. You are receiving this because you authored the thread.Message ID: ***@***.***>

[anki-xyz]

we have since a couple of weeks a quick tip on the main DeepD3 website, leading to this StackOverflow post

[TsungChihTsai]

we have since a couple of weeks a quick tip on the main DeepD3 website, leading to this StackOverflow post

Thanks for your help. I can run this part. However, when I use the code to check the image, it shows:

"---------------------------------------------------------------------------
error Traceback (most recent call last)
in <cell line: 0>()
----> 1 X, Y = dg_training[0]
2 X = X.astype(np.uint8)
3 Y = Y.astype(np.uint8)
4
5 plt.figure(figsize=(12,4))

11 frames
/usr/local/lib/python3.11/dist-packages/deepd3/training/stream.py in getitem(self, index)
87 # Augmenting the data
88 if self.augment:
---> 89 augmented = self.aug(image=image,
90 mask1=dendrite.astype(np.uint8),
91 mask2=spines.astype(np.uint8)) #augment image

/usr/local/lib/python3.11/dist-packages/albumentations/core/composition.py in call(self, force_apply, *args, **data)
494
495 for t in self.transforms:
--> 496 data = t(**data)
497 self._track_transform_params(t, data)
498 data = self.check_data_post_transform(data)

/usr/local/lib/python3.11/dist-packages/albumentations/core/transforms_interface.py in call(self, force_apply, *args, **kwargs)
174 if self.deterministic:
175 kwargs[self.save_key][id(self)] = deepcopy(params)
--> 176 return self.apply_with_params(params, **kwargs)
177
178 return kwargs

/usr/local/lib/python3.11/dist-packages/albumentations/core/transforms_interface.py in apply_with_params(self, params, *args, **kwargs)
198 target_function = self._key2func[key]
199 res[key] = ensure_contiguous_output(
--> 200 target_function(ensure_contiguous_output(arg), **params),
201 )
202 else:

/usr/local/lib/python3.11/dist-packages/albumentations/augmentations/transforms.py in apply(self, img, noise_map, **params)
2262 **params: Any,
2263 ) -> np.ndarray:
-> 2264 return fmain.add_noise(img, noise_map)
2265
2266 def get_params_dependent_on_data(

/usr/local/lib/python3.11/dist-packages/albucore/utils.py in wrapped_function(img, *args, **kwargs)
113 def wrapped_function(img: np.ndarray, *args: P.args, **kwargs: P.kwargs) -> np.ndarray:
114 dtype = img.dtype
--> 115 result = func(img, *args, **kwargs)
116
117 if result.dtype == np.uint8:

/usr/local/lib/python3.11/dist-packages/albumentations/augmentations/functional.py in add_noise(img, noise)
1944 @clipped
1945 def add_noise(img: np.ndarray, noise: np.ndarray) -> np.ndarray:
-> 1946 return add(img, noise, inplace=False)
1947
1948

/usr/local/lib/python3.11/dist-packages/albucore/functions.py in add(img, value, inplace)
269 return add_constant(img, value, inplace)
270
--> 271 return add_vector(img, value, inplace) if value.ndim == 1 else add_array(img, value, inplace)
272
273

/usr/local/lib/python3.11/dist-packages/albucore/utils.py in wrapped_function(img, *args, **kwargs)
113 def wrapped_function(img: np.ndarray, *args: P.args, **kwargs: P.kwargs) -> np.ndarray:
114 dtype = img.dtype
--> 115 result = func(img, *args, **kwargs)
116
117 if result.dtype == np.uint8:

/usr/local/lib/python3.11/dist-packages/albucore/functions.py in add_array(img, value, inplace)
253 @clipped
254 def add_array(img: np.ndarray, value: np.ndarray, inplace: bool = False) -> np.ndarray:
--> 255 return add_opencv(img, value, inplace)
256
257

/usr/local/lib/python3.11/dist-packages/albucore/decorators.py in wrapped_function(img, *args, **kwargs)
40 def wrapped_function(img: np.ndarray, *args: P.args, **kwargs: P.kwargs) -> np.ndarray:
41 shape = img.shape
---> 42 result = func(img, *args, **kwargs)
43 if len(shape) == NUM_MULTI_CHANNEL_DIMENSIONS and shape[-1] == 1 and result.ndim == MONO_CHANNEL_DIMENSIONS:
44 return np.expand_dims(result, axis=-1)

/usr/local/lib/python3.11/dist-packages/albucore/functions.py in add_opencv(img, value, inplace)
228 # Use img as the destination array if inplace=True
229 dst = img if inplace else None
--> 230 return cv2.add(img, value, dst=dst)
231
232

error: OpenCV(4.11.0) /io/opencv/modules/core/src/arithm.cpp:687: error: (-5:Bad argument) When the input arrays in add/subtract/multiply/divide functions have different types, the output array type must be explicitly specified in function 'arithm_op'"