enh: provide download instructions, show series and seg uids

download_instructions.md

@@ -0,0 +1,45 @@
+### Downloading data 
+
+We aim to show a very quick overview on how you can download data with `idc_index` a python package developed by the IDC team to help with basic operations on IDC data.
+
+Learn more @ https://github.com/ImagingDataCommons/idc-idc_index
+
+Detailed Tutorial @ https://github.com/ImagingDataCommons/IDC-Tutorials/blob/master/notebooks/getting_started/part2_searching_basics.ipynb
+
+#### Download idc-index package
+```
+pip install --upgrade idc-index
+```
+
+#### Import module and initialize client
+```
+from idc_index import index
+client = index.IDCClient()
+```
+
+#### Download data
+```
+client.download_from_selection(
+   seriesInstanceUID='<enter your seriesInstanceUID or list of seriesInstanceUIDs>',
+   downloadDir= '<Download destination folder>' )
+
+```
+Below are a couple of examples:
+
+Example 1:
+```
+client.download_from_selection(
+   seriesInstanceUID='1.2.276.0.7230010.3.1.3.313263360.15851.1706325185.577017',
+   downloadDir= 'idc_data' )
+
+```
+
+Example 2:
+```
+client.download_from_selection(
+   seriesInstanceUID=['1.2.276.0.7230010.3.1.3.313263360.15851.1706325185.577017',
+                     '1.2.840.113654.2.55.257926562693607663865369179341285235858'            
+   ],
+   downloadDir= 'idc_data' )
+
+```

filter_data_app.py

@@ -122,6 +122,11 @@ def main():
             instructions = response.text
             st.write(instructions)
 
+        with st.expander("Download instructions using idc-index"):
+            with open("download_instructions.md", "r") as file:
+                instructions = file.read()
+            st.write(instructions)
+
         with st.sidebar:
             st.title("Filters")
 
@@ -328,12 +333,13 @@ def main():
         st.data_editor(
             paginated_df,
             column_config={
-                "Viewer Url":st.column_config.LinkColumn("StudyInstanceUID",
-                              display_text=r"https:\/\/viewer\.imaging\.datacommons\.cancer\.gov\/v3\/viewer\/\?\StudyInstanceUIDs=(.*)&"                               
+                "Viewer Url":st.column_config.LinkColumn("Viewer Url",
+                              #display_text=r"https:\/\/viewer\.imaging\.datacommons\.cancer\.gov\/v3\/viewer\/\?\StudyInstanceUIDs=(.*)&"
+                              display_text='viewerUrl'
                               ),                            
                                           
             },
-            column_order=("PatientID", "Viewer Url", "SeriesNumber","bodyPart","laterality", "segmentation_completeness","laterality_check", "volume_from_voxel_summation_check","connected_components","voxel_num", radiomics_feature),  
+            column_order=("PatientID", "Viewer Url", "CT_SeriesInstanceUID","seg_seriesInstanceUID", "bodyPart","laterality", "segmentation_completeness","laterality_check", "volume_from_voxel_summation_check","connected_components","voxel_num", radiomics_feature),  
             hide_index=True,
             use_container_width=True
         )
@@ -438,7 +444,7 @@ def main():
             response = requests.get(url)
             instructions = response.text
             st.write(instructions)
-  
+
         # Execute the SQL to get summary statistics
         summary_df = duckdb.query("""
             WITH Checks AS (