Extract ROI volume according to new dataset structure

preprocessing/extract_roi_volume_FIXED_SIZE.py → preprocessing/extract_roi_volume.py

+#%%
 import os
 import numpy as np
 import SimpleITK as sitk
 import pandas as pd
+from pathlib import Path
 import sys
+
 PATH = os.path.join(os.path.abspath(os.path.curdir), '..')
 sys.path.append(PATH)
+from tqdm import tqdm
 import dicom_utils.dicom_utils as du
 import dicom_utils.dicom_utils.visualize as viz
 import gc
 
-def to_numpy(image):
-    return(sitk.GetArrayFromImage(image))
+from utils import sitk_to_numpy, filter_outbounds
 
+# os.chdir(PATH)
 #%%
+DATASET_NAME = 'HN_BZ'
+PROJECT_DATA_PATH = Path('data') / DATASET_NAME
+PROCESSED_DATA_PATH = PROJECT_DATA_PATH / 'processed'
+CLINICAL_DATA_FILENAME_CLEAN = f'clinical_{DATASET_NAME}.csv'
+
+DCM_DIR = PROCESSED_DATA_PATH / 'dcm'
+BBOX_OUT_DIR = PROCESSED_DATA_PATH / 'bbox'
+BBOX_SUBDATASET = 'bbox_64'
 
-#PATH = os.path.join(os.path.abspath(os.path.curdir), '..')
-DATA_PATH = '/thunderdisk/HN/'
-DATADIR = f'{DATA_PATH}/data/Head-Neck-PET-CT'
-OUTDIR = f'{DATA_PATH}/processed/bbox_64/'# Destination of processed data (a folder for each patient will be created)
+OUTDIR = BBOX_OUT_DIR / BBOX_SUBDATASET
 
 os.makedirs(OUTDIR, exist_ok=False)
-DIR_INFO_FILE = f'{PATH}/data/summary.csv' # where to find the info about the Original data folders to use 
-ROI_INFO_FILE = f'{PATH}/data/INFO_GTVcontours_HN.csv' # where to find the info about the name of the ROI
 
+
+CT_ranges = [-1050, 3050]
+PT_ranges = [0, 50]
 BOX_SIZE = 64  # mm == pixels for voxel size of 1mm3
-VOXEL_SIZE = [1,1,1]
-HALF_BOX = BOX_SIZE//2
-gaussian = sitk.SmoothingRecursiveGaussianImageFilter()
-gaussian.SetSigma(2)
+VOXEL_SIZE = [1, 1, 1]
+HALF_BOX = BOX_SIZE // 2
+
+# gaussian = sitk.SmoothingRecursiveGaussianImageFilter()
+# gaussian.SetSigma(2)
 
 #%%
-dir_info = pd.read_csv(DIR_INFO_FILE)
-roi_info = pd.read_csv(ROI_INFO_FILE)
+clinical = pd.read_csv(PROCESSED_DATA_PATH / CLINICAL_DATA_FILENAME_CLEAN)
+
+available_patients = patients = [
+    f for f in os.listdir(DCM_DIR) if os.path.isdir(DCM_DIR / f)
+]
 
-subjects = os.listdir(DATADIR)
+clinical = clinical.loc[clinical['patient'].isin(available_patients)]
 
 errors = []
 #%%
-for SUB in subjects:
-    #%%
-    print(SUB)
+for i, row in tqdm(clinical.iterrows()):
+
     try:
-        #%%
-        dir_info_sub = dir_info.query("subject == @SUB")
-        roi_name = roi_info.query('patient == @SUB')['roi_name'].values[0]
+        patient = row['patient']
+        roi_name = row['ROI_name']
+        roi_modality = row['ROI_modality']
+
+        scan_CT = du.load_series(DCM_DIR / patient / 'CT')
+        scan_PT = du.load_SUV(DCM_DIR / patient / 'PT')
 
-        dir_CT = dir_info_sub.query("modality == 'CT'").dir.values[0]
-        dir_PT = dir_info_sub.query("modality == 'PT'").dir.values[0]
-        dir_RT = dir_info_sub.query("modality == 'RTSTRUCT'").dir.values[0]
+        rs_filename = os.listdir(DCM_DIR / patient / 'RTSTRUCT')[0]
 
-        scan_CT = du.load_series(os.path.join(DATADIR, dir_CT))
-        scan_PT = du.load_SUV(os.path.join(DATADIR, dir_PT))
+        if roi_modality == 'CT':
 
-        #%%
-        if 'PETPET' in dir_RT:
-            segmentation = du.load_roi(os.path.join(DATADIR, dir_RT, '000000.dcm'), roi_name, scan_PT)
+            segmentation = du.load_roi(
+                DCM_DIR / patient / 'RTSTRUCT' / rs_filename, roi_name, scan_CT
+            )
+        elif roi_modality == 'PT':
+            segmentation = du.load_roi(
+                DCM_DIR / patient / 'RTSTRUCT' / rs_filename, roi_name, scan_PT
+            )
         else:
-            segmentation = du.load_roi(os.path.join(DATADIR, dir_RT, '000000.dcm'), roi_name, scan_CT)
+            raise ValueError('ROI modality must be `CT` or `PT`.')
 
-        #%%
         start_mm, stop_mm = du.get_bbox_vertices(segmentation)
-        center_mm = (np.array(stop_mm) + np.array(start_mm))/2
+        center_mm = (np.array(stop_mm) + np.array(start_mm)) / 2
 
-        start_mm = center_mm - HALF_BOX - 5 # add margin to allow a better interpolation
+        start_mm = (
+            center_mm - HALF_BOX - 5
+        )  # add margin to allow a better interpolation
         stop_mm = center_mm + HALF_BOX + 5
 
         scan_CT_box = du.extract_volume(scan_CT, start_mm, stop_mm)
+        scan_CT_box = filter_outbounds(scan_CT_box, CT_ranges)
 
-        #%%
         # upsample and register
         scan_CT_box = du.processing.resample(scan_CT_box, spacing=VOXEL_SIZE)
+
         scan_PT_box = sitk.Resample(scan_PT, scan_CT_box)
+        scan_PT_box = filter_outbounds(scan_PT_box, PT_ranges)
+
         # segmentation_box = sitk.Resample(segmentation, scan_CT_box)
         # segmentation_box = gaussian.Execute(segmentation_box)
         # out = segmentation_box>0.5
@@ -81,18 +102,19 @@ for SUB in subjects:
         scan_CT_box = du.extract_volume(scan_CT_box, start_mm, stop_mm)
         scan_PT_box = du.extract_volume(scan_PT_box, start_mm, stop_mm)
 
-        out = np.stack([to_numpy(scan_CT_box), to_numpy(scan_PT_box)], axis = 0)#, to_numpy(segmentation_box)], axis = 0)
+        out = np.stack([sitk_to_numpy(scan_CT_box), sitk_to_numpy(scan_PT_box)], axis=0)
 
-        #save
-        np.save(f'{OUTDIR}/{SUB}.npy', out)
+        # save
+        np.save(f'{OUTDIR}/{patient}.npy', out)
 
         del scan_CT_box, scan_PT_box, segmentation, out
         gc.collect()
 
     except Exception as e:
         print(e)
-        errors.append(SUB)
-        print(f'Error processing sub: {SUB}')
+        errors.append(row['patient'])
+        print(f'Error processing patient: {row["patient"]}')
 
 #%%
 print(errors)
+