How to use when missing files

[xunmzii]

Hi~Due to the missing file 'mimic-cxr-2.0.0-jpeg-txt.csv' , I intend to use the extracted HAIM embeddings you've posted on [https://physionet.org/content/haim-multimodal/1.0.1/] . When I use 'Sample_Multimodal_Patient_Files' in '2_Generate Embeddings from Pickle Files.ipynb', it reports an error : ModuleNotFoundError: No module named 'src' . have already downloaded all the files on this website, and I want to know how to use them in the repo.

[xunmzii]

In 3_Use Embedding for Prediction.ipynb , fname occurs in the second cell without defining or importing packages. So when I run this cell, it reports an error : NameError: name 'fname' is not defined. I wonder what fname means here.

[lrsoenksen]

If you look at the files updated in the Git, you will find there is no dependency on a "src" folder any longer. Also fname is the name of the single embedding files .

[AliRasekh]

Hi,

I also could not load your .pkl files nad I faced the error: ModuleNotFoundError: No module named 'src'. It seems that inside the pickle files there are some paths related to 'src' and it causes this problem. For example when I opened one of the pickle files, it has a content like this: '��
�src.MIMIC_IV_HAIM_API��Patient_ICU���)��}�(�'

@xunmzii Could you handle and open the pickle files at the end?

@lrsoenksen Or can you generate the pickle files again with your updated code and project structure?

Thanks

[lrsoenksen]

Hi @AliRasekh , you have to download the Pickle files from our repo in Physionet, and then position them in the right folder to be loaded

[AliRasekh]

@lrsoenksen

You mean the Sample_Multimodal_Patient_Files Folder in this repo: https://www.physionet.org/content/haim-multimodal/1.0.1/ ?

[lrsoenksen]

Yes, and there it is described how to load them and get the embeddings from them.

[AliRasekh]

I have downloaded the same folder Sample_Multimodal_Patient_Files from this repo: https://www.physionet.org/content/haim-multimodal/1.0.1/

And when I want to load for example this file: 00000004.pkl I get the mentioned error: ModuleNotFoundError: No module named 'src'

And I am using the same method in your code and repo: load_patient_object I have tried both of the code versions(the one in your git repo and the jupyter notebook in the Physionet). But they do not work and I see this error.

[AliRasekh]

If you just put the pickle file in a repo and try to open it with your this method, you will get this error:

def load_patient_object(filepath):
    # Inputs:
    #   filepath -> Pickle file path to save object to
    #
    # Outputs:
    #   obj -> Loaded timebound ICU patient stay object

    # Overwrites any existing file.
    with open(filepath, 'rb') as input:  
        return pickle.load(input)

And as you mentioned in the project there is not src folder or directory. But the error exists.

[lrsoenksen]

I ignore why this is happening, but probably you can fix it by putting a copy of the API (/MIMIC_IV_HAIM_API.py) into a new folder you create in your project called "src", so that you also have the API in the folder where the pickle is complaining src/MIMIC_IV_HAIM_API.py. That should not happen at the pickle file level but that maybe a quick fix.