app.py

import streamlit as st
from streamlit_drawable_canvas import st_canvas
from streamlit_image_coordinates import streamlit_image_coordinates
from idc_index import index
import os
import glob
import shutil
import dcm2niix
import subprocess
import random
import base64

from model.data_process.demo_data_process import process_ct_gt
import numpy as np
import matplotlib.pyplot as plt
from PIL import Image, ImageDraw
import monai.transforms as transforms
from utils import show_points, make_fig, reflect_points_into_model, initial_rectangle, reflect_json_data_to_3D_box, reflect_box_into_model, run
import nibabel as nib
import tempfile

print('script run')
#further improvement
#decorator singletion or use cache data class
# https://docs.streamlit.io/develop/api-reference/caching-and-state/st.experimental_singleton
# https://docs.streamlit.io/develop/concepts/architecture/caching
def download_idc_data_serieUID(serieUID_lst, output_folder):
	#download IDC data cases
	client = index.IDCClient()
  	#define serieUIDs to download
  	#download series and convert to .nii.gz
	if os.path.exists(output_folder):
		shutil.rmtree(output_folder)
	os.makedirs(output_folder)
	for idx, serieUID_ddl in enumerate(serieUID_lst):
		sample_dcm_dir = os.path.join(output_folder, f"ddl_series{idx}_dcm")
		sample_nii_dir = os.path.join(output_folder, f"ddl_series{idx}_nii")
		for dir in [sample_dcm_dir, sample_nii_dir]:
			if os.path.exists(dir):
				shutil.rmtree(dir)
			os.makedirs(dir)
		client.download_from_selection(seriesInstanceUID=serieUID_ddl, downloadDir=sample_dcm_dir)
		subprocess.call(["dcm2niix", "-o", sample_nii_dir, "-z", "y",
		"-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")
	st.session_state.idc_data = True
else:
	case_list = glob.glob("model/asset/idc_samples/*nii/*.nii.gz")
if 'idc_serieUID_sample' not in st.session_state:
	st.session_state.idc_serieUID_sample = None
# init session_state
if 'option' not in  st.session_state:
	st.session_state.option = None
if 'text_prompt' not in st.session_state:
	st.session_state.text_prompt = None
if 'reset_demo_case' not in st.session_state:
	st.session_state.reset_demo_case = False

if 'preds_3D' not in st.session_state:
	st.session_state.preds_3D = None
	st.session_state.preds_3D_ori = None

if 'data_item' not in st.session_state:
	st.session_state.data_item = None

if 'points' not in st.session_state:
	st.session_state.points = []

if 'use_text_prompt' not in st.session_state:
	st.session_state.use_text_prompt = False

if 'use_text_serieUID' not in st.session_state:
	st.session_state.use_text_serieUID = False

if 'use_point_prompt' not in st.session_state:
	st.session_state.use_point_prompt = False

if 'use_box_prompt' not in st.session_state:
	st.session_state.use_box_prompt = False

if 'rectangle_3Dbox' not in st.session_state:
	st.session_state.rectangle_3Dbox = [0,0,0,0,0,0]

if 'irregular_box' not in st.session_state:
	st.session_state.irregular_box = False

if 'running' not in st.session_state:
	st.session_state.running = False

if 'transparency' not in st.session_state:
	st.session_state.transparency = 0.25
#############################################

#############################################
# reset functions
def clear_prompts():
	st.session_state.points = []
	st.session_state.rectangle_3Dbox = [0,0,0,0,0,0]

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()

#############################################
st.image("idc_intro_extended.jpg")
st.write("Below is an example on how to select a SeriesInstanceUID from Imaging Data Commons (IDC) to further use in this demo:")
st.image("https://github.com/ccosmin97/huggingface_idc_demos/raw/main/idc_serieUID_selection.gif")
st.write("Below is an overview of the SegVol method and authors acknowledgement.")
st.image(Image.open('model/asset/overview back.png'), use_column_width=True)

github_col, arxive_col = st.columns(2)

with github_col:
	st.write('SegVol GitHub repo:https://github.com/BAAI-DCAI/SegVol')

with arxive_col:
	st.write('SegVol Paper:https://arxiv.org/abs/2311.13385')


# modify demo case here
demo_type = st.radio(
		"Demo case source",
		["Select an IDC demo case from tcga_lihc collection", 
		"Filter by DICOM SeriesInstanceUID", 
		"Random sampling based on BodyPartExamined"],
		on_change=clear_file
	)

if demo_type=="Select an IDC demo case from tcga_lihc collection":
	uploaded_file = st.selectbox(
		"Select a demo case",
		case_list,
		index=None,
		placeholder="Select a demo case...",
		on_change=reset_demo_case)
elif demo_type=="Filter by DICOM SeriesInstanceUID":
	with st.form("Filter by DICOM SeriesInstanceUID"):
		uploaded_serieUID = st.text_input("Enter a DICOM SeriesInstanceUID", value=None)
		submitted = st.form_submit_button("Submit", on_click=clear_prompts)
		if submitted:
			st.session_state.idc_serieUID_sample  = download_idc_data_serieUID([str(uploaded_serieUID).strip()], "model/asset/idc_serieUID_sample")[0]
			# st.session_state.option = uploaded_file
			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	

if  st.session_state.option is not None and \
	st.session_state.reset_demo_case or (st.session_state.data_item is None and st.session_state.option is not None):

	st.session_state.data_item = process_ct_gt(st.session_state.option)
	st.session_state.reset_demo_case = False
	st.session_state.preds_3D = None
	st.session_state.preds_3D_ori = None

prompt_col1, prompt_col2 = st.columns(2)

with prompt_col1:
	st.session_state.use_text_prompt = st.toggle('Semantic prompt')
	text_prompt_type = st.radio(
		"Semantic prompt type",
		["Predefined", "Custom"],
		disabled=(not st.session_state.use_text_prompt)
	)
	if text_prompt_type == "Predefined":
		pre_text = st.selectbox(
			"Predefined anatomical category:",
			['liver', 'right kidney', 'spleen', 'pancreas', 'aorta', 'inferior vena cava', 'right adrenal gland', 'left adrenal gland', 'gallbladder', 'esophagus', 'stomach', 'duodenum', 'left kidney'],
			index=None,
			disabled=(not st.session_state.use_text_prompt)
		)
	else:
		pre_text = st.text_input('Enter an Anatomical word or phrase:', None, max_chars=20,
													 disabled=(not st.session_state.use_text_prompt))
	if pre_text is None or len(pre_text) > 0:
		st.session_state.text_prompt = pre_text
	else:
		st.session_state.text_prompt = None


with prompt_col2:
	spatial_prompt_on = st.toggle('Spatial prompt', on_change=clear_prompts)
	spatial_prompt = st.radio(
		"Spatial prompt type",
		["Point prompt", "Box prompt"],
		on_change=clear_prompts,
		disabled=(not spatial_prompt_on))
	st.session_state.enforce_zoom = st.checkbox('Enforce zoom-out-zoom-in')

if spatial_prompt == "Point prompt":
	st.session_state.use_point_prompt = True
	st.session_state.use_box_prompt = False
elif spatial_prompt == "Box prompt":
	st.session_state.use_box_prompt = True
	st.session_state.use_point_prompt = False
else:
	st.session_state.use_point_prompt = False
	st.session_state.use_box_prompt = False

if not spatial_prompt_on:
	st.session_state.use_point_prompt = False
	st.session_state.use_box_prompt = False

if not st.session_state.use_text_prompt:
	st.session_state.text_prompt = None

if st.session_state.option is None:
	st.write('please select demo case first')
else:
	image_3D = st.session_state.data_item['z_image'][0].numpy()
	col_control1, col_control2 = st.columns(2)

	with col_control1:
		selected_index_z = st.slider('X-Y view', 0, image_3D.shape[0] - 1, 162, key='xy', disabled=st.session_state.running)

	with col_control2:
		selected_index_y = st.slider('X-Z view', 0, image_3D.shape[1] - 1, 162, key='xz', disabled=st.session_state.running)
		if st.session_state.use_box_prompt:
			top, bottom = st.select_slider(
				'Top and bottom of box',
				options=range(0, 325),
				value=(0, 324),
				disabled=st.session_state.running
			)
			st.session_state.rectangle_3Dbox[0] = top
			st.session_state.rectangle_3Dbox[3] = bottom
	col_image1, col_image2 = st.columns(2)

	if st.session_state.preds_3D is not None:
		st.session_state.transparency = st.slider('Mask opacity', 0.0, 1.0, 0.25, disabled=st.session_state.running)

	with col_image1:

		image_z_array = image_3D[selected_index_z]

		preds_z_array = None
		if st.session_state.preds_3D is not None:
			preds_z_array = st.session_state.preds_3D[selected_index_z]

		image_z = make_fig(image_z_array, preds_z_array, st.session_state.points, selected_index_z, 'xy')


		if st.session_state.use_point_prompt:
			value_xy = streamlit_image_coordinates(image_z, width=325)

			if value_xy is not None:
				point_ax_xy = (selected_index_z, value_xy['y'], value_xy['x'])
				if len(st.session_state.points) >= 3:
					st.warning('Max point num is 3', icon="??")
				elif point_ax_xy not in st.session_state.points:
					st.session_state.points.append(point_ax_xy)
					print('point_ax_xy add rerun')
					st.rerun()
		elif st.session_state.use_box_prompt:
			canvas_result_xy = st_canvas(
				fill_color="rgba(255, 165, 0, 0.3)",  # Fixed fill color with some opacity
				stroke_width=3,
				stroke_color='#2909F1',
				background_image=image_z,
				update_streamlit=True,
				height=325,
				width=325,
				drawing_mode='transform',
				point_display_radius=0,
				key="canvas_xy",
				initial_drawing=initial_rectangle,
				display_toolbar=True
			)
			try:
				print(canvas_result_xy.json_data['objects'][0]['angle'])
				if canvas_result_xy.json_data['objects'][0]['angle'] != 0:
					st.warning('Rotating is undefined behavior', icon="??")
					st.session_state.irregular_box = True
				else:
					st.session_state.irregular_box = False
				reflect_json_data_to_3D_box(canvas_result_xy.json_data, view='xy')
			except:
				print('exception')
				pass
		else:
			st.image(image_z, use_column_width=False)

	with col_image2:
		image_y_array = image_3D[:, selected_index_y, :]

		preds_y_array = None
		if st.session_state.preds_3D is not None:
			preds_y_array = st.session_state.preds_3D[:, selected_index_y, :]

		image_y = make_fig(image_y_array, preds_y_array, st.session_state.points, selected_index_y, 'xz')

		if st.session_state.use_point_prompt:
			value_yz = streamlit_image_coordinates(image_y, width=325)

			if value_yz is not None:
				point_ax_xz = (value_yz['y'], selected_index_y, value_yz['x'])
				if len(st.session_state.points) >= 3:
					st.warning('Max point num is 3', icon="??")
				elif point_ax_xz not in st.session_state.points:
					st.session_state.points.append(point_ax_xz)
					print('point_ax_xz add rerun')
					st.rerun()
		elif st.session_state.use_box_prompt:
			if st.session_state.rectangle_3Dbox[1] <= selected_index_y and selected_index_y <= st.session_state.rectangle_3Dbox[4]:
				draw = ImageDraw.Draw(image_y)
				#rectangle xz view (upper-left and lower-right)
				rectangle_coords = [(st.session_state.rectangle_3Dbox[2], st.session_state.rectangle_3Dbox[0]),
									(st.session_state.rectangle_3Dbox[5], st.session_state.rectangle_3Dbox[3])]
				# Draw the rectangle on the image
				draw.rectangle(rectangle_coords, outline='#2909F1', width=3)
			st.image(image_y, use_column_width=False)
		else:
			st.image(image_y, use_column_width=False)


col1, col2, col3 = st.columns(3)

with col1:
	if st.button("Clear", use_container_width=True,
				 disabled=(st.session_state.option is None or (len(st.session_state.points)==0 and not st.session_state.use_box_prompt and st.session_state.preds_3D is None))):
		clear_prompts()
		st.session_state.preds_3D = None
		st.session_state.preds_3D_ori = None
		st.rerun()

with col2:
	img_nii = None
	if st.session_state.preds_3D_ori is not None and st.session_state.data_item is not None:
		meta_dict = st.session_state.data_item['meta']
		foreground_start_coord = st.session_state.data_item['foreground_start_coord']
		foreground_end_coord = st.session_state.data_item['foreground_end_coord']
		original_shape = st.session_state.data_item['ori_shape']
		pred_array = st.session_state.preds_3D_ori
		original_array = np.zeros(original_shape)
		original_array[foreground_start_coord[0]:foreground_end_coord[0],
					foreground_start_coord[1]:foreground_end_coord[1],
					foreground_start_coord[2]:foreground_end_coord[2]] = pred_array

		original_array = original_array.transpose(2, 1, 0)
		img_nii = nib.Nifti1Image(original_array, affine=meta_dict['affine'])

		with tempfile.NamedTemporaryFile(suffix=".nii.gz") as tmpfile:
			nib.save(img_nii, tmpfile.name)
			with open(tmpfile.name, "rb") as f:
				bytes_data = f.read()
				st.download_button(
					label="Download result(.nii.gz)",
					data=bytes_data,
					file_name="segvol_preds.nii.gz",
					mime="application/octet-stream",
					disabled=img_nii is None
				)

with col3:
	run_button_name = 'Run'if not st.session_state.running else 'Running'
	if st.button(run_button_name, type="primary", use_container_width=True,
			disabled=(
				st.session_state.data_item is None or
				(st.session_state.text_prompt is None and len(st.session_state.points) == 0 and st.session_state.use_box_prompt is False) or
				st.session_state.irregular_box or
				st.session_state.running
				)):
		st.session_state.running = True
		st.rerun()

if st.session_state.running:
	st.session_state.running = False
	with st.status("Running...", expanded=False) as status:
		run()
	st.rerun()