Try to retrieve the procedures of CT scan with contrast
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Description
I am trying to retrieve the procedures of CT scan with contrast.
The procedures_icd file contains the CT scan with contrast records.
I used procedure icd_code to get the CT scan with contrast records.
df = pd.read_csv("d_icd_procedures.csv")
#get the icd_code of CT scan with contrast
df1 = df.loc[df['long_title'].astype(str).str.contains('contrast',na=False, flags=re.IGNORECASE)]
df2 = df1.loc[df1['long_title'].astype(str).str.contains('(CT Scan)',na=False, flags=re.IGNORECASE)]
#icd_code of CT scan with contrast to a list
a = df2['icd_code'].tolist()
separator = '|'
b = separator.join(a)
df2 = pd.read_csv("procedures_icd.csv")
df2 = df2[['subject_id','hadm_id','icd_code']]
#use re to parse the icd_code of CT scan with contrast
df3 = df2.loc[df2['icd_code'].astype(str).str.contains(b,na=False, flags=re.IGNORECASE)]
df3.to_csv("procedure_contrast_id.csv",index=False)
print(df3['hadm_id'].nunique())
There are only 15 records of CT scan with contrast in all MIMIC-IV database! This doesn't make sense. The ratio of CT contrast is too low!
Do I miss anything? or how could I get the CT scan with contrast records?
Thank you very much.
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First steps
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Research direction
Start by running the shown pandas filtering against d_icd_procedures.csv and procedures_icd.csv, focusing on how the ICD codes are combined and matched. Compare the resulting rows with the source procedure records; done means explaining the unexpectedly low count and documenting a reproducible way to retrieve the CT-with-contrast records.
Written by the indexing model from the issue text.
Assessment
- Tech stack
- pandas, python
- Domain
- data, databases
- Issue type
- Bug
- Difficulty
- 3/5
- Estimated time
- 1-2 days
- Activity status
- Stale
- Clarity
- Needs clarification
- Newbie friendliness
- 28/100