Open AmitSharma1127 opened 3 years ago
chunmeifeng
commented
3 years ago Please make sure use the version of pytorchlighting that we have recommended. The IXI is a public dataset, you can obtained from http://brain-development. org/ixi-dataset/. However, the clinical dataset cannot be public because it involves patient privacy.
AmitSharma1127
commented
3 years ago @chunmeifeng Thank you for your response. I am using your recommended version of every package. However, to make it compatible with the GPU, I am using/installing the packages with the following scripts
!pip install numpy==1.18.5 scikit_image==0.16.2 runstats==1.8.0 pytorch_lightning==1.0.6 h5py==2.10.0 PyYAML==5.4
!pip install torch==1.7.0+cu101 torchvision==0.8.1+cu101 -f https://download.pytorch.org/whl/torch_stable.html
!pip install torchtext==0.8
!pip install cloud-tpu-client==0.10 https://storage.googleapis.com/tpu-pytorch/wheels/torch_xla-1.7-cp37-cp37m-linux_x86_64.whlPlease let me know if this is the right way to run the code on Google Colab.
Also, if you would shed light on the exact pre-processing steps and any other useful information that might be required to re-implement this, and that's not already shared by you in your paper, please help me with that. Thank you.
chunmeifeng
commented
3 years ago Is the code running yet? You must use the pytorchlighting version that we have recommend, I have tried that will some error if you use other version.
Amit Sharma @.***> 于2021年7月5日周一 上午4:31写道：
@chunmeifeng https://github.com/chunmeifeng Thank you for your response. I am using your recommended version of every package. However, to make it compatible with the GPU, I am using/installing the packages with the following scripts
!pip install numpy==1.18.5 scikit_image==0.16.2 runstats==1.8.0 pytorch_lightning==1.0.6 h5py==2.10.0 PyYAML==5.4 !pip install torch==1.7.0+cu101 torchvision==0.8.1+cu101 -f https://download.pytorch.org/whl/torch_stable.html !pip install torchtext==0.8 !pip install cloud-tpu-client==0.10 https://storage.googleapis.com/tpu-pytorch/wheels/torch_xla-1.7-cp37-cp37m-linux_x86_64.whl
Please let me know if this is the right way to run the code on Google Colab.
Also, if you would shed light on the exact pre-processing steps and any other useful information that might be required to re-implement this, and that's not already shared by you in your paper, please help me with that. Thank you.
— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/chunmeifeng/T2Net/issues/2#issuecomment-873697308, or unsubscribe https://github.com/notifications/unsubscribe-auth/AR75XN7UXXCK3C3QW7TVWJ3TWD4NPANCNFSM47WZRS5Q .
AmitSharma1127
commented
3 years ago @chunmeifeng No, I am still not able to run the code. I am using the recommended version of pytorchlightening == 1.0.6.
Also, if you would shed light on the exact pre-processing steps and any other useful information that might be required to re-implement this, and that's not already shared by you in your paper, please help me with that. Thank you.
Would you please comment on the above as well?
chunmeifeng
commented
3 years ago can you tell me which error when you run the code？
Amit Sharma @.***> 于 2021年7月6日周二 下午5:19写道：
@chunmeifeng https://github.com/chunmeifeng No, I am still not able to run the code. I am using the recommended version of pytorchlightening == 1.0.6.
Also, if you would shed light on the exact pre-processing steps and any other useful information that might be required to re-implement this, and that's not already shared by you in your paper, please help me with that. Thank you.
Would you please comment on the above as well?
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AmitSharma1127
commented
3 years ago can you tell me which error when you run the code？
The same one in my original comment:
Following the previous issue (#1) updates. I am faced with the above mentioned runtime error. This happens when I run the code in the GPU runtime. The stack-trace is as follows:
Traceback (most recent call last): File "/usr/local/lib/python3.7/dist-packages/pytorch_lightning/utilities/xla_device_utils.py", line 30, in inner_f queue.put(func(*args, **kwargs)) File "/usr/local/lib/python3.7/dist-packages/pytorch_lightning/utilities/xla_device_utils.py", line 81, in _is_device_tpu device = xm.xla_device() File "/usr/local/lib/python3.7/dist-packages/torch_xla/core/xla_model.py", line 231, in xla_device devkind=devkind if devkind is not None else None) File "/usr/local/lib/python3.7/dist-packages/torch_xla/core/xla_model.py", line 136, in get_xla_supported_devices xla_devices = _DEVICES.value File "/usr/local/lib/python3.7/dist-packages/torch_xla/utils/utils.py", line 32, in value self._value = self._gen_fn() File "/usr/local/lib/python3.7/dist-packages/torch_xla/core/xla_model.py", line 18, in <lambda> _DEVICES = xu.LazyProperty(lambda: torch_xla._XLAC._xla_get_devices()) RuntimeError: tensorflow/compiler/xla/xla_client/computation_client.cc:274 : Missing XLA configuration Traceback (most recent call last): File "/usr/local/lib/python3.7/dist-packages/pytorch_lightning/utilities/xla_device_utils.py", line 30, in inner_f queue.put(func(*args, **kwargs)) File "/usr/local/lib/python3.7/dist-packages/pytorch_lightning/utilities/xla_device_utils.py", line 81, in _is_device_tpu device = xm.xla_device() File "/usr/local/lib/python3.7/dist-packages/torch_xla/core/xla_model.py", line 231, in xla_device devkind=devkind if devkind is not None else None) File "/usr/local/lib/python3.7/dist-packages/torch_xla/core/xla_model.py", line 136, in get_xla_supported_devices xla_devices = _DEVICES.value File "/usr/local/lib/python3.7/dist-packages/torch_xla/utils/utils.py", line 32, in value self._value = self._gen_fn() File "/usr/local/lib/python3.7/dist-packages/torch_xla/core/xla_model.py", line 18, in <lambda> _DEVICES = xu.LazyProperty(lambda: torch_xla._XLAC._xla_get_devices()) RuntimeError: tensorflow/compiler/xla/xla_client/computation_client.cc:274 : Missing XLA configuration Traceback (most recent call last): File "/usr/local/lib/python3.7/dist-packages/pytorch_lightning/utilities/xla_device_utils.py", line 30, in inner_f queue.put(func(*args, **kwargs)) File "/usr/local/lib/python3.7/dist-packages/pytorch_lightning/utilities/xla_device_utils.py", line 81, in _is_device_tpu device = xm.xla_device() File "/usr/local/lib/python3.7/dist-packages/torch_xla/core/xla_model.py", line 231, in xla_device devkind=devkind if devkind is not None else None) File "/usr/local/lib/python3.7/dist-packages/torch_xla/core/xla_model.py", line 136, in get_xla_supported_devices xla_devices = _DEVICES.value File "/usr/local/lib/python3.7/dist-packages/torch_xla/utils/utils.py", line 32, in value self._value = self._gen_fn() File "/usr/local/lib/python3.7/dist-packages/torch_xla/core/xla_model.py", line 18, in <lambda> _DEVICES = xu.LazyProperty(lambda: torch_xla._XLAC._xla_get_devices()) RuntimeError: tensorflow/compiler/xla/xla_client/computation_client.cc:274 : Missing XLA configuration Traceback (most recent call last): File "/usr/local/lib/python3.7/dist-packages/pytorch_lightning/utilities/xla_device_utils.py", line 30, in inner_f queue.put(func(*args, **kwargs)) File "/usr/local/lib/python3.7/dist-packages/pytorch_lightning/utilities/xla_device_utils.py", line 81, in _is_device_tpu device = xm.xla_device() File "/usr/local/lib/python3.7/dist-packages/torch_xla/core/xla_model.py", line 231, in xla_device devkind=devkind if devkind is not None else None) File "/usr/local/lib/python3.7/dist-packages/torch_xla/core/xla_model.py", line 136, in get_xla_supported_devices xla_devices = _DEVICES.value File "/usr/local/lib/python3.7/dist-packages/torch_xla/utils/utils.py", line 32, in value self._value = self._gen_fn() File "/usr/local/lib/python3.7/dist-packages/torch_xla/core/xla_model.py", line 18, in <lambda> _DEVICES = xu.LazyProperty(lambda: torch_xla._XLAC._xla_get_devices()) RuntimeError: tensorflow/compiler/xla/xla_client/computation_client.cc:274 : Missing XLA configurationThis should be noted that the above error goes away if I change the runtime to TPU. However, the rest of the code seems to be dependent on GPU runtime.
What am I doing wrong?
AmitSharma1127
commented
3 years ago For better understanding, I am sharing the collab that I am working on: https://colab.research.google.com/drive/1-KBTZXXAKkXnUCIwMYDcfkyKoVqim5UH?usp=sharing
AmitSharma1127
commented
3 years ago Also, where can I get/ how can I generate the "1D-Cartesian_6X_128128.mat" and "1D-Random-3X_256.mat" as mentioned in the fastmri.mri_ixi_t2net.py file? I believe there's no explanation for these 2 files in the paper.
chunmeifeng
commented
3 years ago Can you tell me your personal email address? I will send you the mask through email.
Amit Sharma @.***> 于2021年7月7日周三 下午4:51写道：
Also, where can I get/ how can I generate the "1D-Cartesian_6X_128128.mat" and "1D-Random-3X_256.mat" as mentioned in the fastmri.mri_ixi_t2net.py file? I believe there's no explanation for these 2 files in the paper.
— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/chunmeifeng/T2Net/issues/2#issuecomment-875576076, or unsubscribe https://github.com/notifications/unsubscribe-auth/AR75XNZN3GEFXQWMPF7VZWLTWREUPANCNFSM47WZRS5Q .
AmitSharma1127
commented
3 years ago Sure! amitsharma1127@gmail.com
Thank you so much!
chunmeifeng
commented
3 years ago please ask yunlu to get the mask @.***
YunxinLiu @.***> 于2021年7月29日周四 上午11:22写道：
Hello, thank you for sharing such a nice work. Can you please send me the mask file to my email, thank you very much for your help ! My @.***
— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/chunmeifeng/T2Net/issues/2#issuecomment-888868071, or unsubscribe https://github.com/notifications/unsubscribe-auth/AR75XNY7S7MINOH6QLOOAUDT2D6VBANCNFSM47WZRS5Q .
Aristot1e
commented
2 years ago Can you tell me your personal email address? I will send you the mask through email.
Amit Sharma @.***> 于2021年7月7日周三 下午4:51写道：
Also, where can I get/ how can I generate the "1D-Cartesian_6X_128128.mat" and "1D-Random-3X_256.mat" as mentioned in the fastmri.mri_ixi_t2net.py file? I believe there's no explanation for these 2 files in the paper.
— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/chunmeifeng/T2Net/issues/2#issuecomment-875576076, or unsubscribe https://github.com/notifications/unsubscribe-auth/AR75XNZN3GEFXQWMPF7VZWLTWREUPANCNFSM47WZRS5Q .
Hello, thank you for sharing such a nice work. Can you please send me the mask file to my email, thank you very much for your help ! My email:2020110200@mail.scuec.edu.can
chunmeifeng
commented
2 years ago Please find the mask through https://github.com/chunmeifeng/T2Net
Aristot1e @.***> 于2021年11月7日周日 上午10:13写道：
Can you tell me your personal email address? I will send you the mask through email.
Amit Sharma @.***> 于2021年7月7日周三 下午4:51写道：
Also, where can I get/ how can I generate the "1D-Cartesian_6X_128128.mat" and "1D-Random-3X_256.mat" as mentioned in the fastmri.mri_ixi_t2net.py file? I believe there's no explanation for these 2 files in the paper.
— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub
2 (comment)
https://github.com/chunmeifeng/T2Net/issues/2#issuecomment-875576076, or unsubscribe
https://github.com/notifications/unsubscribe-auth/AR75XNZN3GEFXQWMPF7VZWLTWREUPANCNFSM47WZRS5Q .
Hello, thank you for sharing such a nice work. Can you please send me the mask file to my email, thank you very much for your help ! My @.***
— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/chunmeifeng/T2Net/issues/2#issuecomment-962576236, or unsubscribe https://github.com/notifications/unsubscribe-auth/AR75XNY2MLPCG473D3342FDUKY7NDANCNFSM47WZRS5Q . Triage notifications on the go with GitHub Mobile for iOS https://apps.apple.com/app/apple-store/id1477376905?ct=notification-email&mt=8&pt=524675 or Android https://play.google.com/store/apps/details?id=com.github.android&referrer=utm_campaign%3Dnotification-email%26utm_medium%3Demail%26utm_source%3Dgithub.
Aristot1e
commented
2 years ago Please find the mask through https://github.com/chunmeifeng/T2Net
Aristot1e @.***> 于2021年11月7日周日 上午10:13写道：
Can you tell me your personal email address? I will send you the mask through email.
Amit Sharma @.***> 于2021年7月7日周三 下午4:51写道：
Also, where can I get/ how can I generate the "1D-Cartesian_6X_128128.mat" and "1D-Random-3X_256.mat" as mentioned in the fastmri.mri_ixi_t2net.py file? I believe there's no explanation for these 2 files in the paper.
— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub
2 (comment)
https://github.com/chunmeifeng/T2Net/issues/2#issuecomment-875576076, or unsubscribe
https://github.com/notifications/unsubscribe-auth/AR75XNZN3GEFXQWMPF7VZWLTWREUPANCNFSM47WZRS5Q .
Hello, thank you for sharing such a nice work. Can you please send me the mask file to my email, thank you very much for your help ! My @.***
— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/chunmeifeng/T2Net/issues/2#issuecomment-962576236, or unsubscribe https://github.com/notifications/unsubscribe-auth/AR75XNY2MLPCG473D3342FDUKY7NDANCNFSM47WZRS5Q . Triage notifications on the go with GitHub Mobile for iOS https://apps.apple.com/app/apple-store/id1477376905?ct=notification-email&mt=8&pt=524675 or Android https://play.google.com/store/apps/details?id=com.github.android&referrer=utm_campaign%3Dnotification-email%26utm_medium%3Demail%26utm_source%3Dgithub.
I can't find the 1D-Random-3x_256.mat and could you send me this file?/ how can I get this?
chunmeifeng
commented
2 years ago yunlu will send you this mask.
Aristot1e @.***> 于2021年11月8日周一 下午2:53写道：
Please find the mask through https://github.com/chunmeifeng/T2Net
Aristot1e @.***> 于2021年11月7日周日 上午10:13写道：
Can you tell me your personal email address? I will send you the mask through email.
Amit Sharma @.***> 于2021年7月7日周三 下午4:51写道：
Also, where can I get/ how can I generate the "1D-Cartesian_6X_128128.mat" and "1D-Random-3X_256.mat" as mentioned in the fastmri.mri_ixi_t2net.py file? I believe there's no explanation for these 2 files in the paper.
— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub
2 https://github.com/chunmeifeng/T2Net/issues/2 (comment)
2 (comment)
https://github.com/chunmeifeng/T2Net/issues/2#issuecomment-875576076, or unsubscribe
https://github.com/notifications/unsubscribe-auth/AR75XNZN3GEFXQWMPF7VZWLTWREUPANCNFSM47WZRS5Q .
Hello, thank you for sharing such a nice work. Can you please send me the mask file to my email, thank you very much for your help ! My @.***
— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub
2 (comment)
https://github.com/chunmeifeng/T2Net/issues/2#issuecomment-962576236, or unsubscribe
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I can't find the 1D-Random-3x_256.mat and could you send me this file?/ how can I get this?
— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/chunmeifeng/T2Net/issues/2#issuecomment-963170432, or unsubscribe https://github.com/notifications/unsubscribe-auth/AR75XNYEETQQOQ723VNUTALUK7I55ANCNFSM47WZRS5Q . Triage notifications on the go with GitHub Mobile for iOS https://apps.apple.com/app/apple-store/id1477376905?ct=notification-email&mt=8&pt=524675 or Android https://play.google.com/store/apps/details?id=com.github.android&referrer=utm_campaign%3Dnotification-email%26utm_medium%3Demail%26utm_source%3Dgithub.
1632325673
commented
2 years ago 你好，请问可以给我分享文件中提到的“1D-Random-3X_256.mat” 文件吗，我的邮箱是1632325673@qq.com，非常感谢
chunmeifeng
commented
2 years ago Hi yunlu, please send the mask to him.
1632325673 @.***> 于2021年11月10日周三 上午9:21写道：
你好，请问可以给我分享文件中提到的“1D-Random-3X_256.mat” @.***，非常感谢
— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/chunmeifeng/T2Net/issues/2#issuecomment-964886102, or unsubscribe https://github.com/notifications/unsubscribe-auth/AR75XN6QXU3VS23AV3MOJULULITRBANCNFSM47WZRS5Q . Triage notifications on the go with GitHub Mobile for iOS https://apps.apple.com/app/apple-store/id1477376905?ct=notification-email&mt=8&pt=524675 or Android https://play.google.com/store/apps/details?id=com.github.android&referrer=utm_campaign%3Dnotification-email%26utm_medium%3Demail%26utm_source%3Dgithub.
chunmeifeng
commented
2 years ago Hi friends, you can find the mask file here https://github.com/chunmeifeng/T2Net
Aristot1e @.***> 于2021年11月16日周二 上午9:19写道：
Hello, thank you for sharing such a nice work. Can you please send me the mask file to my email, thank you very much for your help ! My email: @.***
Hi friend, have you got this mask file? And have you reproduced this code? We can talk about this.
— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/chunmeifeng/T2Net/issues/2#issuecomment-970006383, or unsubscribe https://github.com/notifications/unsubscribe-auth/AR75XNYCG6EQ6QGKGVNEIW3UMIH2RANCNFSM47WZRS5Q . Triage notifications on the go with GitHub Mobile for iOS https://apps.apple.com/app/apple-store/id1477376905?ct=notification-email&mt=8&pt=524675 or Android https://play.google.com/store/apps/details?id=com.github.android&referrer=utm_campaign%3Dnotification-email%26utm_medium%3Demail%26utm_source%3Dgithub.
windfall666
commented
1 year ago 你好，请问可以给我分享文件中提到的“1D-Random-3X_256.mat” 文件吗，我的邮箱是1160827902@qq.com，非常感谢！
chunmeifeng
commented
1 year ago 链接中已经提供了的 windfall666 @.***>于2022年11月29日 周二18:31写道：
你好，请问可以给我分享文件中提到的“1D-Random-3X_256.mat” @.***，非常感谢！
— Reply to this email directly, view it on GitHub https://github.com/chunmeifeng/T2Net/issues/2#issuecomment-1330416182, or unsubscribe https://github.com/notifications/unsubscribe-auth/AR75XN5FQ5V6GR6ZX7AM6FTWKXLOXANCNFSM47WZRS5Q . You are receiving this because you were mentioned.Message ID: @.***>
windfall666
commented
1 year ago 十分感谢！
------------------ 原始邮件 ------------------ 发件人: "chunmeifeng/T2Net" @.>; 发送时间: 2022年11月29日(星期二) 晚上6:38 @.>; @.**@.>; 主题: Re: [chunmeifeng/T2Net] RuntimeError: tensorflow/compiler/xla/xla_client/computation_client.cc:274 : Missing XLA configuration (#2)
链接中已经提供了的 windfall666 @.***>于2022年11月29日 周二18:31写道：
> 你好，请问可以给我分享文件中提到的“1D-Random-3X_256.mat” @.，非常感谢！ > > — > Reply to this email directly, view it on GitHub > <https://github.com/chunmeifeng/T2Net/issues/2#issuecomment-1330416182>, > or unsubscribe > <https://github.com/notifications/unsubscribe-auth/AR75XN5FQ5V6GR6ZX7AM6FTWKXLOXANCNFSM47WZRS5Q> > . > You are receiving this because you were mentioned.Message ID: > @.> >
— Reply to this email directly, view it on GitHub, or unsubscribe. You are receiving this because you commented.Message ID: @.***>
Following the previous issue (https://github.com/chunmeifeng/T2Net/issues/1) updates. I am faced with the above mentioned runtime error. This happens when I run the code in the GPU runtime. The stack-trace is as follows:
This should be noted that the above error goes away if I change the runtime to TPU. However, the rest of the code seems to be dependent on GPU runtime.
What am I doing wrong?