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lihaoliu-cambridge / mtmr-net

[TMI'19 & DLMIA'18] Code for "Multi-Task Deep Learning with Margin Ranking Loss for Lung Nodule Analysis".
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code #2

Closed huliangxiao closed 6 months ago

huliangxiao commented 5 years ago

hello, i'm confused about the code below, the dateset don't provide the csv and pkl file

  1. file_list = glob(original_data_path + "Images_3/" + "*.mhd")
  2. csv_info = pd.read_csv(os.path.join(original_csvfiles_path, "CSVFILES", "annotations_xml_voxel.csv"))
  3. f = open("/home/lhliu/Onepiece/project/PythonProjects/bmdiagnosis_research/data/" "output_data/preprocessing_related/LIDC_mask_all.pkl")

please tell where is wrong, thanks a lot!

lihaoliu-cambridge commented 5 years ago

It is a middle file which is produced during the data generating stage.

This file contains information of all lung nodules from the original xml file .

Please see https://github.com/jcausey-astate/NoduleX_code for generating the datasets from the original datas.

huliangxiao commented 5 years ago

thanks, i'll try~

huliangxiao commented 5 years ago

does the csv_and_feature_file_tools folder generate the .csv and .pkl file? and what is the *mhd? i don't find the code.

sorry for bothering, but i really need ur help.

lihaoliu-cambridge commented 5 years ago

No, the .mhd file is the 3D volume preprocessed from the original LIDC-IDRI dataset.

These files are generated by my own preprocessing code which is modified based on NoduleX's code.

I think you can follow this part from NoduleX directly since I cannot find my data generating codes.

Besides, you can modify that code to create your own.

It is basically a process that crops small lung nodules from the entire body (3D volumes) and records its benign-malignancy and other information in a csv file.

huliangxiao commented 5 years ago

ok, thank you!

shuyao-zhang commented 4 years ago

hello，im confused about “LIDC_mask_all.pkl” This code exists in the preprocessing phase，where can i generate this .pkl file？perhaps ，where can i download this file？ I would like to know the processing relationship between each folder. i really need your help,thank you very much!

lihaoliu-cambridge commented 4 years ago

This is a generated middle-stage data by me. It contains the information about the lung nodules.

I have remove it from the project in GitHub since I am not allow to redistribute data.

Those information can be found in original datasets.

Please follow the given links for data preprocessing.

On 9 Apr 2020, at 9:07 AM, shuyao-zhang notifications@github.com wrote:

hello，im confused about “LIDC_mask_all.pkl” This code exists in the preprocessing phase，where can i generate this .pkl file？perhaps ，where can i download this file？ I would like to know the processing relationship between each folder. i really need your help,thank you very much!

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