update app.py -- added random sampling by BodyPartExamined

added random sampling by BodyPartExamined

BodyPartExamined is as of now defined in a static manner, due to large variability in orientation and dcm2niix behaviour, in the future use idc_index to retrieve all lists and incorporate sanity checks.

app.py

@@ -7,6 +7,7 @@ import glob
 import shutil
 import dcm2niix
 import subprocess
+import random
 
 from model.data_process.demo_data_process import process_ct_gt
 import numpy as np
@@ -42,19 +43,46 @@ def download_idc_data_serieUID(serieUID_lst, output_folder):
 		"-f", "IDC_%i", "-g", "y", sample_dcm_dir])
 	return glob.glob(os.path.join(output_folder, "*nii/*.nii.gz"))
 
+
+def get_random_sample_idc_from_bodypart(bodypart_selected):
+	client = index.IDCClient()
+	# body_parts = client.index[(client.index['Modality'].isin(['CT']))&(idc_client.index['instanceCount']> '100')]['BodyPartExamined'].unique()
+	matching_series_list = client.index[client.index['Modality'].isin(["CT"]) \
+				& (client.index['BodyPartExamined'] == bodypart_selected) & \
+				(client.index['instanceCount']> '100')]['SeriesInstanceUID'].values
+	# select random series from the list
+	random_series_uid = random.choice(matching_series_list)
+	random_series_viewer_url = client.get_viewer_URL(random_series_uid)
+	return random_series_uid, random_series_viewer_url
+
+def retrieve_idc_index_body_parts():
+	idc_client = index.IDCClient()
+	body_parts = idc_client.index[(idc_client.index['Modality'].isin(['CT']))&(idc_client.index['instanceCount']< '150')]['BodyPartExamined'].unique()
+	return body_parts
+	
 #############################################
 st.session_state.option = None
 
 if 'idc_data' not in st.session_state:
-	case_list = download_idc_data_serieUID(serieUID_lst=["1.3.6.1.4.1.14519.5.2.1.8421.4008.125612661111422710051062993644",
-	                "1.3.6.1.4.1.14519.5.2.1.3344.4008.552105302448832783460360105045",
-	                "1.3.6.1.4.1.14519.5.2.1.3344.4008.217290429362492484143666931850",
-	                "1.3.6.1.4.1.14519.5.2.1.3344.4008.315023636447426194723399171147",
-	                "1.3.6.1.4.1.14519.5.2.1.3344.4008.307374355712319704057189924161"],
-										output_folder="model/asset/idc_samples")
+	# case_list = download_idc_data_serieUID(serieUID_lst=["1.3.6.1.4.1.14519.5.2.1.8421.4008.125612661111422710051062993644",
+	#                 "1.3.6.1.4.1.14519.5.2.1.3344.4008.552105302448832783460360105045",
+	#                 "1.3.6.1.4.1.14519.5.2.1.3344.4008.217290429362492484143666931850",
+	#                 "1.3.6.1.4.1.14519.5.2.1.3344.4008.315023636447426194723399171147",
+	#                 "1.3.6.1.4.1.14519.5.2.1.3344.4008.307374355712319704057189924161"],
+	# 									output_folder="model/asset/idc_samples")
+	case_list = []
 	st.session_state.idc_data = True
 else:
 	case_list = glob.glob("model/asset/idc_samples/*nii/*.nii.gz")
+# if 'idc_index_body_part' not in st.session_state:
+# 	body_part_list = retrieve_idc_index_body_parts()
+# 	st.session_state.idc_index_body_part = True
+# else:
+# 	body_part_list = [""]
+# if 'init_idc_client' not in st.session_state:
+# 	st.session_state.idc_client = index.IDCClient()
+# if 'idc_bodypart_selected' not in st.session_state:
+# 	st.session_state.idc_bodypart_selected = False
 if 'idc_serieUID_sample' not in st.session_state:
 	st.session_state.idc_serieUID_sample = None
 # init session_state
@@ -110,11 +138,13 @@ def reset_demo_case():
 	st.session_state.data_item = None
 	st.session_state.idc_serieUID_sample = None
 	st.session_state.reset_demo_case = True
+	st.session_state.idc_bodypart_selected = False
 	clear_prompts()
 
 def clear_file():
 	st.session_state.option = None
 	st.session_state.idc_serieUID_sample = None
+	st.session_state.idc_bodypart_selected = False
 	process_ct_gt.clear()
 	reset_demo_case()
 	clear_prompts()
@@ -135,7 +165,9 @@ with arxive_col:
 # modify demo case here
 demo_type = st.radio(
 		"Demo case source",
-		["Select an IDC demo case from tcga_lihc collection", "Filter by DICOM SerieUID"],
+		["Select an IDC demo case from tcga_lihc collection", 
+		"Filter by DICOM SeriesInstanceUID", 
+		"Random sampling based on BodyPartExamined"],
 		on_change=clear_file
 	)
 
@@ -146,7 +178,7 @@ if demo_type=="Select an IDC demo case from tcga_lihc collection":
 		index=None,
 		placeholder="Select a demo case...",
 		on_change=reset_demo_case)
-else:
+elif demo_type=="Filter by DICOM SeriesInstanceUID":
 	with st.form("Filter by DICOM SerieUID"):
 		uploaded_serieUID = st.text_input("Enter a DICOM SeriesInstanceUID", value=None)
 		submitted = st.form_submit_button("Submit", on_click=clear_prompts)
@@ -156,6 +188,34 @@ else:
 			uploaded_file = st.session_state.idc_serieUID_sample
 		else:
 			uploaded_file = st.session_state.idc_serieUID_sample
+else:#elif demo_type == "Random sampling based on BodyPartExamined":
+	with st.form("Filter by DICOM BodyPartExamined Tag") as form_body_part:
+		# body_part_list = retrieve_idc_index_body_parts()
+		body_part_selected = st.selectbox(
+			"Select a bodypart to randomly sample a CT scan from",
+			["ABDOMEN", "LUNG", "LIVER",
+			"PELVIS"],
+			index=None,
+			placeholder="Select a bodypart to pick a SeriesInstanceUID from...")
+		submitted = st.form_submit_button("Submit", on_click=reset_demo_case)
+		#if st.session_state.reset_demo_case == True and body_part_selected is not None:# and st.session_state.idc_bodypart_selected == False and 
+		if submitted:	
+			serieUID, ohif_link = get_random_sample_idc_from_bodypart(body_part_selected)
+			for i in range(0,5):
+				if os.path.exists("model/asset/idc_serieUID_random_sample"):
+					shutil.rmtree("model/asset/idc_serieUID_random_sample")
+				st.session_state.idc_serieUID_sample  = download_idc_data_serieUID([str(serieUID)], "model/asset/idc_serieUID_random_sample")[0]
+				path_file = glob.glob(f"model/asset/idc_serieUID_random_sample/ddl_series0_nii/*.nii.gz")
+				if path_file  and len(path_file) == 1:
+					break
+				else:
+					print("serieUID NOT FILLING BASIC REQs --> MORE THAN 1 NII FILE OR NO NII FILE")
+			# st.write(f"SeriesInstanceUID randomly sampled from chosen BodyPartExamined : {random_series_uid}")
+			# st.write(f"OHIF URL of selected sample : {random_series_viewer_url}")
+			# st.session_state.idc_bodypart_selected = True
+			uploaded_file = st.session_state.idc_serieUID_sample
+		else:
+			uploaded_file = st.session_state.idc_serieUID_sample
 
 st.session_state.option = uploaded_file