Comments (8)
heraldofsolace
commented on June 24, 2024
Try Tensorlfow 1.4.0
from cellseg.
Jimut123
commented on June 24, 2024
ERROR: Could not find a version that satisfies the requirement tensorflow==1.4.0 (from versions: 1.13.0rc1, 1.13.0rc2, 1.13.1, 1.13.2, 1.14.0rc0, 1.14.0rc1, 1.14.0, 1.15.0rc0, 1.15.0rc1, 1.15.0rc2, 1.15.0rc3, 1.15.0, 1.15.2, 1.15.3, 1.15.4, 1.15.5, 2.0.0a0, 2.0.0b0, 2.0.0b1, 2.0.0rc0, 2.0.0rc1, 2.0.0rc2, 2.0.0, 2.0.1, 2.0.2, 2.0.3, 2.0.4, 2.1.0rc0, 2.1.0rc1, 2.1.0rc2, 2.1.0, 2.1.1, 2.1.2, 2.1.3, 2.2.0rc0, 2.2.0rc1, 2.2.0rc2, 2.2.0rc3, 2.2.0rc4, 2.2.0, 2.2.1, 2.2.2, 2.3.0rc0, 2.3.0rc1, 2.3.0rc2, 2.3.0, 2.3.1, 2.3.2, 2.4.0rc0, 2.4.0rc1, 2.4.0rc2, 2.4.0rc3, 2.4.0rc4, 2.4.0, 2.4.1)
ERROR: No matching distribution found for tensorflow==1.4.0
from cellseg.
Jimut123
commented on June 24, 2024
ARNING:tensorflow:From /home/tamal/anaconda3/envs/aniket_mask_rcnn3/lib/python3.7/site-packages/tensorflow/python/compat/compat.py:175: disable_resource_variables (from tensorflow.python.ops.variable_scope) is deprecated and will be removed in a future version.
Instructions for updating:
non-resource variables are not supported in the long term
Using TensorFlow backend.
WARNING:tensorflow:From /home/tamal/anaconda3/envs/aniket_mask_rcnn3/lib/python3.7/site-packages/tensorflow/python/framework/op_def_library.py:263: colocate_with (from tensorflow.python.framework.ops) is deprecated and will be removed in a future version.
Instructions for updating:
Colocations handled automatically by placer.
2021-03-17 18:19:00.090136: I tensorflow/core/platform/cpu_feature_guard.cc:141] Your CPU supports instructions that this TensorFlow binary was not compiled to use: AVX2 FMA
2021-03-17 18:19:00.117074: I tensorflow/core/platform/profile_utils/cpu_utils.cc:94] CPU Frequency: 3699850000 Hz
2021-03-17 18:19:00.117502: I tensorflow/compiler/xla/service/service.cc:150] XLA service 0x5572f17545d0 executing computations on platform Host. Devices:
2021-03-17 18:19:00.117526: I tensorflow/compiler/xla/service/service.cc:158] StreamExecutor device (0): ,
/content/dataset/basophil/train/images
Traceback (most recent call last):
File "mask_rcnn3.py", line 273, in
train(model, "/content/dataset")
File "mask_rcnn3.py", line 218, in train
dataset_train.load_blood(dataset_dir, "train")
File "mask_rcnn3.py", line 171, in load_blood
image_ids = list(map(lambda x: x.split('.')[0], next(os.walk(image_dir))[2]))
StopIteration
from cellseg.
Jimut123
commented on June 24, 2024
Starting at epoch 0. LR=0.001
Checkpoint Path: /home/tamal/Research/Jimut/bloseg/Aniket_MASK_RCNN/MaskRCNN_3/Mask_RCNN/logs/blood20210317T1820/mask_rcnn_blood_{epoch:04d}.h5
Selecting layers to train
fpn_c5p5 (Conv2D)
fpn_c4p4 (Conv2D)
fpn_c3p3 (Conv2D)
fpn_c2p2 (Conv2D)
fpn_p5 (Conv2D)
fpn_p2 (Conv2D)
fpn_p3 (Conv2D)
fpn_p4 (Conv2D)
In model: rpn_model
rpn_conv_shared (Conv2D)
rpn_class_raw (Conv2D)
rpn_bbox_pred (Conv2D)
mrcnn_mask_conv1 (TimeDistributed)
mrcnn_mask_bn1 (TimeDistributed)
mrcnn_mask_conv2 (TimeDistributed)
mrcnn_mask_bn2 (TimeDistributed)
mrcnn_class_conv1 (TimeDistributed)
mrcnn_class_bn1 (TimeDistributed)
mrcnn_mask_conv3 (TimeDistributed)
mrcnn_mask_bn3 (TimeDistributed)
mrcnn_class_conv2 (TimeDistributed)
mrcnn_class_bn2 (TimeDistributed)
mrcnn_mask_conv4 (TimeDistributed)
mrcnn_mask_bn4 (TimeDistributed)
mrcnn_bbox_fc (TimeDistributed)
mrcnn_mask_deconv (TimeDistributed)
mrcnn_class_logits (TimeDistributed)
mrcnn_mask (TimeDistributed)
Traceback (most recent call last):
File "mask_rcnn3.py", line 273, in
train(model, "./dataset")
File "mask_rcnn3.py", line 246, in train
layers='heads')
File "/home/tamal/Research/Jimut/bloseg/Aniket_MASK_RCNN/MaskRCNN_3/Mask_RCNN/mrcnn/model.py", line 2354, in train
self.compile(learning_rate, self.config.LEARNING_MOMENTUM)
File "/home/tamal/Research/Jimut/bloseg/Aniket_MASK_RCNN/MaskRCNN_3/Mask_RCNN/mrcnn/model.py", line 2199, in compile
self.keras_model.add_metric(loss, name)
AttributeError: 'Model' object has no attribute 'add_metric'
from cellseg.
Jimut123
commented on June 24, 2024
/home/tamal/anaconda3/envs/aniket_mask_rcnn3/lib/python3.7/site-packages/tensorboard/compat/tensorflow_stub/dtypes.py:541: FutureWarning: Passing (type, 1) or '1type' as a synonym of type is deprecated; in a future version of numpy, it will be understood as (type, (1,)) / '(1,)type'.
_np_qint8 = np.dtype([("qint8", np.int8, 1)])
/home/tamal/anaconda3/envs/aniket_mask_rcnn3/lib/python3.7/site-packages/tensorboard/compat/tensorflow_stub/dtypes.py:542: FutureWarning: Passing (type, 1) or '1type' as a synonym of type is deprecated; in a future version of numpy, it will be understood as (type, (1,)) / '(1,)type'.
_np_quint8 = np.dtype([("quint8", np.uint8, 1)])
/home/tamal/anaconda3/envs/aniket_mask_rcnn3/lib/python3.7/site-packages/tensorboard/compat/tensorflow_stub/dtypes.py:543: FutureWarning: Passing (type, 1) or '1type' as a synonym of type is deprecated; in a future version of numpy, it will be understood as (type, (1,)) / '(1,)type'.
_np_qint16 = np.dtype([("qint16", np.int16, 1)])
/home/tamal/anaconda3/envs/aniket_mask_rcnn3/lib/python3.7/site-packages/tensorboard/compat/tensorflow_stub/dtypes.py:544: FutureWarning: Passing (type, 1) or '1type' as a synonym of type is deprecated; in a future version of numpy, it will be understood as (type, (1,)) / '(1,)type'.
_np_quint16 = np.dtype([("quint16", np.uint16, 1)])
/home/tamal/anaconda3/envs/aniket_mask_rcnn3/lib/python3.7/site-packages/tensorboard/compat/tensorflow_stub/dtypes.py:545: FutureWarning: Passing (type, 1) or '1type' as a synonym of type is deprecated; in a future version of numpy, it will be understood as (type, (1,)) / '(1,)type'.
_np_qint32 = np.dtype([("qint32", np.int32, 1)])
/home/tamal/anaconda3/envs/aniket_mask_rcnn3/lib/python3.7/site-packages/tensorboard/compat/tensorflow_stub/dtypes.py:550: FutureWarning: Passing (type, 1) or '1type' as a synonym of type is deprecated; in a future version of numpy, it will be understood as (type, (1,)) / '(1,)type'.
np_resource = np.dtype([("resource", np.ubyte, 1)])
WARNING:tensorflow:From /home/tamal/anaconda3/envs/aniket_mask_rcnn3/lib/python3.7/site-packages/tensorflow_core/python/compat/v2_compat.py:68: disable_resource_variables (from tensorflow.python.ops.variable_scope) is deprecated and will be removed in a future version.
Instructions for updating:
non-resource variables are not supported in the long term
Using TensorFlow backend.
WARNING:tensorflow:From /home/tamal/anaconda3/envs/aniket_mask_rcnn3/lib/python3.7/site-packages/keras/backend/tensorflow_backend.py:541: The name tf.placeholder is deprecated. Please use tf.compat.v1.placeholder instead.
WARNING:tensorflow:From /home/tamal/anaconda3/envs/aniket_mask_rcnn3/lib/python3.7/site-packages/keras/backend/tensorflow_backend.py:66: The name tf.get_default_graph is deprecated. Please use tf.compat.v1.get_default_graph instead.
WARNING:tensorflow:From /home/tamal/anaconda3/envs/aniket_mask_rcnn3/lib/python3.7/site-packages/keras/backend/tensorflow_backend.py:4432: The name tf.random_uniform is deprecated. Please use tf.random.uniform instead.
WARNING:tensorflow:From /home/tamal/anaconda3/envs/aniket_mask_rcnn3/lib/python3.7/site-packages/keras/backend/tensorflow_backend.py:2139: The name tf.nn.fused_batch_norm is deprecated. Please use tf.compat.v1.nn.fused_batch_norm instead.
WARNING:tensorflow:From /home/tamal/anaconda3/envs/aniket_mask_rcnn3/lib/python3.7/site-packages/keras/backend/tensorflow_backend.py:4267: The name tf.nn.max_pool is deprecated. Please use tf.nn.max_pool2d instead.
WARNING:tensorflow:From /home/tamal/anaconda3/envs/aniket_mask_rcnn3/lib/python3.7/site-packages/keras/backend/tensorflow_backend.py:2239: The name tf.image.resize_nearest_neighbor is deprecated. Please use tf.compat.v1.image.resize_nearest_neighbor instead.
WARNING:tensorflow:From /home/tamal/anaconda3/envs/aniket_mask_rcnn3/lib/python3.7/site-packages/tensorflow_core/python/ops/array_ops.py:1475: where (from tensorflow.python.ops.array_ops) is deprecated and will be removed in a future version.
Instructions for updating:
Use tf.where in 2.0, which has the same broadcast rule as np.where
WARNING:tensorflow:From /home/tamal/anaconda3/envs/aniket_mask_rcnn3/lib/python3.7/site-packages/mask_rcnn-2.1-py3.7.egg/mrcnn/model.py:553: The name tf.random_shuffle is deprecated. Please use tf.random.shuffle instead.
WARNING:tensorflow:From /home/tamal/anaconda3/envs/aniket_mask_rcnn3/lib/python3.7/site-packages/mask_rcnn-2.1-py3.7.egg/mrcnn/utils.py:202: The name tf.log is deprecated. Please use tf.math.log instead.
WARNING:tensorflow:From /home/tamal/anaconda3/envs/aniket_mask_rcnn3/lib/python3.7/site-packages/mask_rcnn-2.1-py3.7.egg/mrcnn/model.py:600: calling crop_and_resize_v1 (from tensorflow.python.ops.image_ops_impl) with box_ind is deprecated and will be removed in a future version.
Instructions for updating:
box_ind is deprecated, use box_indices instead
WARNING:tensorflow:From /home/tamal/anaconda3/envs/aniket_mask_rcnn3/lib/python3.7/site-packages/keras/backend/tensorflow_backend.py:190: The name tf.get_default_session is deprecated. Please use tf.compat.v1.get_default_session instead.
WARNING:tensorflow:From /home/tamal/anaconda3/envs/aniket_mask_rcnn3/lib/python3.7/site-packages/keras/backend/tensorflow_backend.py:197: The name tf.ConfigProto is deprecated. Please use tf.compat.v1.ConfigProto instead.
WARNING:tensorflow:From /home/tamal/anaconda3/envs/aniket_mask_rcnn3/lib/python3.7/site-packages/keras/backend/tensorflow_backend.py:203: The name tf.Session is deprecated. Please use tf.compat.v1.Session instead.
2021-03-17 18:26:22.000920: I tensorflow/core/platform/cpu_feature_guard.cc:142] Your CPU supports instructions that this TensorFlow binary was not compiled to use: AVX2 FMA
2021-03-17 18:26:22.021257: I tensorflow/core/platform/profile_utils/cpu_utils.cc:94] CPU Frequency: 3699850000 Hz
2021-03-17 18:26:22.021639: I tensorflow/compiler/xla/service/service.cc:168] XLA service 0x5651c7f85910 initialized for platform Host (this does not guarantee that XLA will be used). Devices:
2021-03-17 18:26:22.021686: I tensorflow/compiler/xla/service/service.cc:176] StreamExecutor device (0): Host, Default Version
WARNING:tensorflow:From /home/tamal/anaconda3/envs/aniket_mask_rcnn3/lib/python3.7/site-packages/keras/backend/tensorflow_backend.py:207: The name tf.global_variables is deprecated. Please use tf.compat.v1.global_variables instead.
WARNING:tensorflow:From /home/tamal/anaconda3/envs/aniket_mask_rcnn3/lib/python3.7/site-packages/keras/backend/tensorflow_backend.py:216: The name tf.is_variable_initialized is deprecated. Please use tf.compat.v1.is_variable_initialized instead.
WARNING:tensorflow:From /home/tamal/anaconda3/envs/aniket_mask_rcnn3/lib/python3.7/site-packages/keras/backend/tensorflow_backend.py:223: The name tf.variables_initializer is deprecated. Please use tf.compat.v1.variables_initializer instead.
2021-03-17 18:26:23.662876: W tensorflow/core/framework/cpu_allocator_impl.cc:81] Allocation of 51380224 exceeds 10% of system memory.
./dataset/basophil/train/images
./dataset/eosinophil/train/images
./dataset/erythroblast/train/images
./dataset/ig/train/images
./dataset/lymphocyte/train/images
./dataset/monocyte/train/images
./dataset/neutrophil/train/images
./dataset/platelet/train/images
./dataset/basophil/val/images
./dataset/eosinophil/val/images
./dataset/erythroblast/val/images
./dataset/ig/val/images
./dataset/lymphocyte/val/images
./dataset/monocyte/val/images
./dataset/neutrophil/val/images
./dataset/platelet/val/images
Train network heads
Starting at epoch 0. LR=0.001
Checkpoint Path: /home/tamal/Research/Jimut/bloseg/Aniket_MASK_RCNN/MaskRCNN_3/Mask_RCNN/logs/blood20210317T1826/mask_rcnn_blood_{epoch:04d}.h5
Selecting layers to train
fpn_c5p5 (Conv2D)
fpn_c4p4 (Conv2D)
fpn_c3p3 (Conv2D)
fpn_c2p2 (Conv2D)
fpn_p5 (Conv2D)
fpn_p2 (Conv2D)
fpn_p3 (Conv2D)
fpn_p4 (Conv2D)
In model: rpn_model
rpn_conv_shared (Conv2D)
rpn_class_raw (Conv2D)
rpn_bbox_pred (Conv2D)
mrcnn_mask_conv1 (TimeDistributed)
mrcnn_mask_bn1 (TimeDistributed)
mrcnn_mask_conv2 (TimeDistributed)
mrcnn_mask_bn2 (TimeDistributed)
mrcnn_class_conv1 (TimeDistributed)
mrcnn_class_bn1 (TimeDistributed)
mrcnn_mask_conv3 (TimeDistributed)
mrcnn_mask_bn3 (TimeDistributed)
mrcnn_class_conv2 (TimeDistributed)
mrcnn_class_bn2 (TimeDistributed)
mrcnn_mask_conv4 (TimeDistributed)
mrcnn_mask_bn4 (TimeDistributed)
mrcnn_bbox_fc (TimeDistributed)
mrcnn_mask_deconv (TimeDistributed)
mrcnn_class_logits (TimeDistributed)
mrcnn_mask (TimeDistributed)
WARNING:tensorflow:From /home/tamal/anaconda3/envs/aniket_mask_rcnn3/lib/python3.7/site-packages/keras/optimizers.py:793: The name tf.train.Optimizer is deprecated. Please use tf.compat.v1.train.Optimizer instead.
Traceback (most recent call last):
File "mask_rcnn3.py", line 273, in <module>
train(model, "./dataset")
File "mask_rcnn3.py", line 246, in train
layers='heads')
File "/home/tamal/anaconda3/envs/aniket_mask_rcnn3/lib/python3.7/site-packages/mask_rcnn-2.1-py3.7.egg/mrcnn/model.py", line 2354, in train
File "/home/tamal/anaconda3/envs/aniket_mask_rcnn3/lib/python3.7/site-packages/mask_rcnn-2.1-py3.7.egg/mrcnn/model.py", line 2199, in compile
AttributeError: 'Model' object has no attribute 'add_metric'
from cellseg.
Jimut123
commented on June 24, 2024
/home/tamal/anaconda3/envs/aniket_mask_rcnn3/lib/python3.7/site-packages/skimage/transform/_warps.py:830: FutureWarning: Input image dtype is bool. Interpolation is not defined with bool data type. Please set order to 0 or explicitely cast input image to another data type. Starting from version 0.19 a ValueError will be raised instead of this warning.
order = _validate_interpolation_order(image.dtype, order)
/home/tamal/anaconda3/envs/aniket_mask_rcnn3/lib/python3.7/site-packages/skimage/transform/_warps.py:830: FutureWarning: Input image dtype is bool. Interpolation is not defined with bool data type. Please set order to 0 or explicitely cast input image to another data type. Starting from version 0.19 a ValueError will be raised instead of this warning.
order = _validate_interpolation_order(image.dtype, order)
/home/tamal/anaconda3/envs/aniket_mask_rcnn3/lib/python3.7/site-packages/skimage/transform/_warps.py:830: FutureWarning: Input image dtype is bool. Interpolation is not defined with bool data type. Please set order to 0 or explicitely cast input image to another data type. Starting from version 0.19 a ValueError will be raised instead of this warning.
order = _validate_interpolation_order(image.dtype, order)
/home/tamal/anaconda3/envs/aniket_mask_rcnn3/lib/python3.7/site-packages/skimage/transform/_warps.py:830: FutureWarning: Input image dtype is bool. Interpolation is not defined with bool data type. Please set order to 0 or explicitely cast input image to another data type. Starting from version 0.19 a ValueError will be raised instead of this warning.
order = _validate_interpolation_order(image.dtype, order)
/home/tamal/anaconda3/envs/aniket_mask_rcnn3/lib/python3.7/site-packages/skimage/transform/_warps.py:830: FutureWarning: Input image dtype is bool. Interpolation is not defined with bool data type. Please set order to 0 or explicitely cast input image to another data type. Starting from version 0.19 a ValueError will be raised instead of this warning.
order = _validate_interpolation_order(image.dtype, order)
/home/tamal/anaconda3/envs/aniket_mask_rcnn3/lib/python3.7/site-packages/skimage/transform/_warps.py:830: FutureWarning: Input image dtype is bool. Interpolation is not defined with bool data type. Please set order to 0 or explicitely cast input image to another data type. Starting from version 0.19 a ValueError will be raised instead of this warning.
order = _validate_interpolation_order(image.dtype, order)
/home/tamal/anaconda3/envs/aniket_mask_rcnn3/lib/python3.7/site-packages/skimage/transform/_warps.py:830: FutureWarning: Input image dtype is bool. Interpolation is not defined with bool data type. Please set order to 0 or explicitely cast input image to another data type. Starting from version 0.19 a ValueError will be raised instead of this warning.
order = _validate_interpolation_order(image.dtype, order)
/home/tamal/anaconda3/envs/aniket_mask_rcnn3/lib/python3.7/site-packages/skimage/transform/_warps.py:830: FutureWarning: Input image dtype is bool. Interpolation is not defined with bool data type. Please set order to 0 or explicitely cast input image to another data type. Starting from version 0.19 a ValueError will be raised instead of this warning.
order = _validate_interpolation_order(image.dtype, order)
from cellseg.
Jimut123
commented on June 24, 2024
pip install -U scikit-image==0.16.2
from cellseg.
Jimut123
commented on June 24, 2024
Lol managed to run but will take 20 mins per epochs with the current RAM. Looks CUDA isn't installed
from cellseg.
Related Issues (14)
- Refactoring of Code, Proper Folder Structure and Add new codes uptill progress HOT 31
- Data store link for reference HOT 5
- EOSINOPHILS started
- LYMPHOCYTES started
- METAMYELOCYTES started
- MONOCYTES started
- PROMYELOCYTES started
- Colors
- Slides to Mask using CVAT HOT 22
- New error while upgrading to tensorflow-gpu for faster eval HOT 1
- No history neither models or generated images saved, we need to save model, history and generated images HOT 7
- Annotation
- Proper data store HOT 1
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from cellseg.