uiowaSEP2024 · mbrzus · Feb 9, 2024 · Feb 8, 2024 · Feb 8, 2024 · Feb 8, 2024
diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
@@ -12,3 +12,11 @@ repos:
     rev: 22.10.0
     hooks:
     -   id: black
+- repo: https://github.com/astral-sh/ruff-pre-commit
+    # Ruff version.
+  rev: v0.2.1
+  hooks:
+  # Run the linter.
+  - id: ruff
+    args: [ --fix , --ignore , "F403" ]
+    exclude: "__init__"
diff --git a/example_tool/brainmask_tool.py b/example_tool/brainmask_tool.py
@@ -3,14 +3,12 @@
 import argparse
 
 import pydicom
-from pdf2dcm import Pdf2EncapsDCM, Pdf2RgbSC
+from pdf2dcm import Pdf2EncapsDCM
 from subprocess import run
-from pipeline_functions import *
+from pipeline_functions import dicom_inference_and_conversion, brainmask_inference
 from pdf_report import generate_report
 from pydicom import dcmread
 from pathlib import Path
-from enum import Enum, auto
-
 
 
 description = "author: Michal Brzus\nBrainmask Tool\n"
@@ -51,7 +49,7 @@
 output_path = Path(args.output_dir)
 
 
-try :
+try:
     nifti_path = dicom_inference_and_conversion(
         session_dir=session_path.as_posix(),
         output_dir=output_path.as_posix(),
@@ -101,7 +99,9 @@
 mask_path = list(Path(brainmask_output_dir).glob("*.nii.gz"))[0]
 stage_name = "report_generation"
 try:
-    pdf_fn = generate_report(im_path.as_posix(), mask_path.as_posix(), report_output_dir)
+    pdf_fn = generate_report(
+        im_path.as_posix(), mask_path.as_posix(), report_output_dir
+    )
     print(f"Report created: {pdf_fn}")
 except Exception as e:
     print(f"Error in stage: {stage_name}")
@@ -114,22 +114,23 @@
 
 try:
     converter = Pdf2EncapsDCM()
-    converted_dcm = converter.run(path_pdf=pdf_fn, path_template_dcm=template_dcm.as_posix(), suffix =".dcm")[0]
+    converted_dcm = converter.run(
+        path_pdf=pdf_fn, path_template_dcm=template_dcm.as_posix(), suffix=".dcm"
+    )[0]
     del report_output_dir, brainmask_output_dir, nifti_path
 
     print(f"Report created: {converted_dcm}")
 
     # Adding needed metadata to the report
     """"""
-    pdf_dcm = dcmread(converted_dcm,stop_before_pixels=True)
-
+    pdf_dcm = dcmread(converted_dcm, stop_before_pixels=True)
 
     extra_metadata = [
-    (
-        "SeriesDescription",
-        "0008,103e",
-        f"This is a rough brainmask",
-    ),
+        (
+            "SeriesDescription",
+            "0008,103e",
+            "This is a rough brainmask",
+        ),
     ]
     for info in extra_metadata:
         title = info[0]
@@ -148,4 +149,4 @@
 print(f"Successfully finished stage: {stage_name}")
 
 
-# [ 'tests/test_data/test_file.dcm' ]
+# [ 'tests/test_data/test_file.dcm' ]
diff --git a/example_tool/cnn_transforms.py b/example_tool/cnn_transforms.py
@@ -150,8 +150,8 @@ def __call__(self, data):
         return d
 
 
-unsqueze_lambda = lambda x: x.squeeze(dim=0)
-shape_lambda = lambda x: x.shape
+# unsqueze_lambda = lambda x: x.squeeze(dim=0)
+# shape_lambda = lambda x: x.shape
 
 
 class ResampleMaskToOgd(object):

diff --git a/example_tool/pdf_report.py b/example_tool/pdf_report.py
@@ -6,8 +6,6 @@
 import numpy as np
 from io import BytesIO
 import base64
-import subprocess
-import platform
 
 
 # CSS Content
@@ -102,8 +100,7 @@ def generate_image(im_path, mask_path):
     return image_base64
 
 
-def generate_pdf(brain_volume, image_base64, file_path
-):
+def generate_pdf(brain_volume, image_base64, file_path):
     # HTML Content
     html_string = f"""
     <!DOCTYPE html>

diff --git a/example_tool/pipeline_functions.py b/example_tool/pipeline_functions.py
@@ -1,30 +1,34 @@
-from cnn_transforms import *
+from cnn_transforms import (
+    LoadITKImaged,
+    ResampleStartRegionBrainMaskd,
+    ITKImageToNumpyd,
+    AddChanneld,
+    ToITKImaged,
+    ResampleMaskToOgd,
+    SaveITKImaged,
+)
 import pytorch_lightning as pl
 from monai.data import CacheDataset
-
 from monai.networks.layers import Norm
 from monai.networks.nets import UNet
 from monai.transforms import (
     Compose,
     ScaleIntensityRangePercentilesd,
     ToTensord,
     CopyItemsd,
-    KeepLargestConnectedComponentd,
-    FillHolesd
 )
-from torchmetrics.classification import Dice
 import torch
-from monai.losses.dice import GeneralizedDiceFocalLoss
-
-itk.MultiThreaderBase.SetGlobalDefaultNumberOfThreads(1)
-
 from pathlib import Path
 from dcm_classifier.study_processing import ProcessOneDicomStudyToVolumesMappingBase
 from dcm_classifier.image_type_inference import ImageTypeClassifierBase
 from dcm_classifier.namic_dicom_typing import itk_read_from_dicomfn_list
 import re
 from pydicom import dcmread
 from subprocess import run
+import itk
+
+
+itk.MultiThreaderBase.SetGlobalDefaultNumberOfThreads(1)
 
 
 def validate_subject_id(subject_id: str) -> str:
@@ -82,9 +86,13 @@ def dicom_inference_and_conversion(
             fname = f"{validate_subject_id(sub)}_{validate_session_id(ses)}_acq-{plane}_{modality}"
             series_vol_list = series.get_volume_list()
             if len(series_vol_list) > 1:
-                print(f"Series {series_number} not supported. More than one volume in series.")
+                print(
+                    f"Series {series_number} not supported. More than one volume in series."
+                )
             else:
-                itk_im = itk_read_from_dicomfn_list(series_vol_list[0].get_one_volume_dcm_filenames())
+                itk_im = itk_read_from_dicomfn_list(
+                    series_vol_list[0].get_one_volume_dcm_filenames()
+                )
                 itk.imwrite(itk_im, f"{sub_ses_dir}/{fname}.nii.gz")
 
     return sub_ses_dir
@@ -108,7 +116,9 @@ def forward(self, x):
         return self.model(x)
 
 
-def brainmask_inference(data: list, model_file: str, out_dir: str, postfix='brainmask') -> None:
+def brainmask_inference(
+    data: list, model_file: str, out_dir: str, postfix="brainmask"
+) -> None:
     print("\nDATA: ", data)
     model = BrainmaskModel.load_from_checkpoint(
         checkpoint_path=model_file,
@@ -155,12 +165,10 @@ def brainmask_inference(data: list, model_file: str, out_dir: str, postfix='brai
         with torch.no_grad():  # perform the inference
             test_output = model.model(item["image"].unsqueeze(dim=0).to(device))
             # convert from one hot encoding
-            out_im = (
-                torch.argmax(test_output, dim=1).detach().cpu()
-            )
+            out_im = torch.argmax(test_output, dim=1).detach().cpu()
 
         print(out_im.shape)
-        item["inferred_label"] = out_im #.squeeze(dim=0)
+        item["inferred_label"] = out_im  # .squeeze(dim=0)
         item["inferred_label_meta_dict"] = item["image_meta_dict"]
         item["inferred_label_meta_dict"]["filename"] = item["image_meta_dict"][
             "filename"
@@ -176,4 +184,3 @@ def brainmask_inference(data: list, model_file: str, out_dir: str, postfix='brai
             ]
         )
         out_transforms(item)
-
diff --git a/job-monitoring-app/backend/app/models/api_key.py b/job-monitoring-app/backend/app/models/api_key.py
@@ -1,4 +1,4 @@
-from sqlalchemy import Column, Integer, String, ForeignKey, DateTime, func
+from sqlalchemy import Column, Integer, String, ForeignKey, DateTime
 from sqlalchemy.orm import relationship
 
 from .base import Base, DateMixin

diff --git a/job-monitoring-app/backend/app/models/event.py b/job-monitoring-app/backend/app/models/event.py
@@ -1,5 +1,5 @@
 from sqlalchemy import Column, ForeignKey
-from sqlalchemy.sql.sqltypes import String, Integer, Enum, JSON
+from sqlalchemy.sql.sqltypes import String, Integer, Enum
 from sqlalchemy.dialects.postgresql import JSONB
 from sqlalchemy.orm import relationship
 

diff --git a/job-monitoring-app/backend/app/models/job.py b/job-monitoring-app/backend/app/models/job.py
@@ -1,6 +1,6 @@
 from sqlalchemy import Column, ForeignKey, UniqueConstraint
 from sqlalchemy.sql.sqltypes import String, Integer
-from sqlalchemy.orm import relationship, backref
+from sqlalchemy.orm import relationship
 
 from .base import Base, DateMixin
 

diff --git a/job-monitoring-app/backend/app/models/metadata_configuration.py b/job-monitoring-app/backend/app/models/metadata_configuration.py
@@ -1,4 +1,4 @@
-from sqlalchemy import Column, Enum, ForeignKey, UniqueConstraint
+from sqlalchemy import Column, Enum, ForeignKey
 from sqlalchemy.orm import relationship
 from sqlalchemy.sql.sqltypes import Integer, String
 

diff --git a/job-monitoring-app/backend/app/routers/api_keys.py b/job-monitoring-app/backend/app/routers/api_keys.py
@@ -2,11 +2,10 @@
     get_db,
     get_user_from_api_key,
     API_KEY_HEADER_NAME,
-    get_current_user_from_token,
     get_current_provider,
 )
 from app import schemas, services
-from fastapi import APIRouter, Depends, Query
+from fastapi import APIRouter, Depends
 from sqlalchemy.orm import Session
 
 router = APIRouter()

diff --git a/job-monitoring-app/backend/app/routers/events.py b/job-monitoring-app/backend/app/routers/events.py
@@ -1,6 +1,6 @@
 from app import schemas, services
 from app.dependencies import get_db, get_user_from_api_key
-from fastapi import APIRouter, Depends, HTTPException
+from fastapi import APIRouter, Depends
 from sqlalchemy.orm import Session
 
 router = APIRouter()

diff --git a/job-monitoring-app/backend/app/routers/job_configurations.py b/job-monitoring-app/backend/app/routers/job_configurations.py
@@ -38,7 +38,7 @@ def get_job_configuration_by_id(
     if job_configuration is None:
         raise HTTPException(status_code=404, detail="Job not found")
 
-    if not (provider.id in [job_configuration.provider_id]):
+    if provider.id not in [job_configuration.provider_id]:
         raise HTTPException(status_code=403, detail="Not allowed")
 
     return job_configuration
@@ -53,7 +53,7 @@ def get_job_configurations_by_tag_and_version(
 ):
     # case 1: get specific configuration if both tag and version are provided
     should_get_specific_version_of_tag = tag and (
-        type(version) is str and version != "latest"
+        isinstance(version, str) and version != "latest"
     )
 
     if should_get_specific_version_of_tag:

diff --git a/job-monitoring-app/backend/app/routers/jobs.py b/job-monitoring-app/backend/app/routers/jobs.py
@@ -42,7 +42,7 @@ def get_job(
     if job is None:
         raise HTTPException(status_code=404, detail="Job not found")
 
-    if not (user.id in [job.customer_id, job.provider_id]):
+    if user.id not in [job.customer_id, job.provider_id]:
         # TODO: add job.provider_id to the list of allowed users that can
         #  access this once we have api key based access? See above comment
         raise HTTPException(status_code=403, detail="Not allowed")
@@ -62,7 +62,7 @@ def get_job_events(
     if job is None:
         raise HTTPException(status_code=404, detail="Job not found")
 
-    if not (user.id in [job.customer_id, job.provider_id]):
+    if user.id not in [job.customer_id, job.provider_id]:
         raise HTTPException(status_code=403, detail="Not allowed")
 
     return job.events
diff --git a/job-monitoring-app/backend/app/routers/reporting.py b/job-monitoring-app/backend/app/routers/reporting.py
@@ -1,10 +1,9 @@
 from datetime import datetime, timedelta
 
-from app import schemas, services
+from app import services
 from app.dependencies import get_db, get_current_provider
-from fastapi import APIRouter, Depends, HTTPException
+from fastapi import APIRouter, Depends
 from sqlalchemy.orm import Session
-from fastapi import FastAPI
 from fastapi.responses import StreamingResponse
 import io
 import pandas as pd

diff --git a/job-monitoring-app/backend/app/schemas/event.py b/job-monitoring-app/backend/app/schemas/event.py
@@ -2,7 +2,7 @@
 from enum import Enum
 from typing import Dict, Optional, Union
 
-from pydantic import BaseModel, Json
+from pydantic import BaseModel
 
 from .step_configuration import StepConfiguration
 

diff --git a/job-monitoring-app/backend/app/schemas/job.py b/job-monitoring-app/backend/app/schemas/job.py
@@ -1,7 +1,7 @@
 from datetime import datetime
 from typing import List
 
-from pydantic import BaseModel, StrictStr
+from pydantic import BaseModel
 
 from . import Event
 from .job_configuration import JobConfiguration

diff --git a/job-monitoring-app/backend/app/schemas/step_configuration.py b/job-monitoring-app/backend/app/schemas/step_configuration.py
@@ -1,7 +1,7 @@
 from datetime import datetime
 from typing import List, Optional
 
-from pydantic import StrictInt, StrictStr, conlist
+from pydantic import StrictInt, StrictStr
 
 from .metadata_configuration import MetadataConfiguration, MetadataConfigurationCreate
 from .unique_tag import UniqueTagModel

diff --git a/job-monitoring-app/backend/app/services/api_keys.py b/job-monitoring-app/backend/app/services/api_keys.py
@@ -10,7 +10,6 @@
 
 from datetime import datetime
 
-from .users import get_user
 
 pwd_context = CryptContext(schemes=["bcrypt"], deprecated="auto")
 

diff --git a/job-monitoring-app/backend/app/services/events.py b/job-monitoring-app/backend/app/services/events.py
@@ -1,5 +1,4 @@
 from app import models, schemas
-from sqlalchemy import cast
 from sqlalchemy.orm import Session
 
 from .job_configuration import get_step_configuration_by_composite_key

diff --git a/job-monitoring-app/backend/app/services/reporting.py b/job-monitoring-app/backend/app/services/reporting.py
@@ -1,5 +1,5 @@
 import json
-from datetime import datetime, timedelta
+from datetime import datetime
 
 from pydantic import BaseModel
 from sqlalchemy.orm import Session

diff --git a/job-monitoring-app/backend/conftest.py b/job-monitoring-app/backend/conftest.py
@@ -1,6 +1,3 @@
-import os
-import random
-
 import pytest
 from app import schemas, services, models
 from app.models.base import truncate_all_tables
Original file line number	Diff line number	Diff line change
Expand Up		@@ -10,7 +10,6 @@

		from datetime import datetime

		from .users import get_user

		pwd_context = CryptContext(schemes=["bcrypt"], deprecated="auto")

Expand Down