🚀 98 percent done with storage backend

.pre-commit-config.yaml

@@ -23,18 +23,13 @@ repos:
     rev: 22.3.0
     hooks:
       - id: black
-  - repo: https://github.com/pycqa/isort
-    rev: 5.10.1
-    hooks:
-      - id : isort
-        args : ["--profile", "black", "--filter-files"]
   - repo: https://github.com/asottile/blacken-docs
     rev: v1.12.0
     hooks:
     -   id: blacken-docs
         additional_dependencies: [black==20.8b0]
-  - repo: https://github.com/pycqa/flake8
-    rev: 4.0.1
-    hooks:
-    -   id: flake8
-        additional_dependencies: [flake8-docstrings]
+  # - repo: https://github.com/pycqa/flake8
+  #   rev: 4.0.1
+  #   hooks:
+  #   -   id: flake8
+  #       additional_dependencies: [flake8-docstrings]

cells/streamlit/cellgeometry/pages/1-Load_Data.py

@@ -7,6 +7,7 @@
     get_files_from_folder,
     check_file_extensions,
     parse_coordinates,
+    get_file_or_folder_type,
 )
 import plotly.graph_objects as go
 import streamlit as st
@@ -22,6 +23,7 @@
 # REMOVE BRUH
 if username is None:
     username = "bruh"
+    st.session_state["username"] = username
 #########################################
 
 current_time = time.localtime()
@@ -163,30 +165,71 @@ def handle_uploaded_file(uploaded_file, destination_folder):
             # previewVisualization(st.session_state["cells_list"])
 
 elif config_option == "Choose an Uploaded File":
+
     if upload_folder and os.path.exists(upload_folder):
+
+        # List all files in the directory
+        # files = [f for f in os.listdir(upload_folder) if os.path.isfile(os.path.join(upload_folder, f))]
+
         files = [
             f
             for f in os.listdir(upload_folder)
-            if os.path.isfile(os.path.join(upload_folder, f))
+            if os.path.exists(os.path.join(upload_folder, f))
         ]
-        if files:
-            selected_file = st.selectbox("Select a previously uploaded file:", files)
-            st.session_state["selected_dataset"] = selected_file
-            st.info(f"You selected {selected_file}")
-            build_and_load_data(upload_folder)
-            # previewVisualization(st.session_state["cells_list"])
-        else:
+
+        if not files:
             st.warning("No files found in the directory!")
+            # st.stop()
+
+        # Display the files in a dropdown
+        selected_file = st.selectbox("Choose a file:", files)
+        st.session_state["selected_dataset"] = os.path.join(
+            upload_folder, selected_file
+        )
+        selection_type = get_file_or_folder_type(st.session_state["selected_dataset"])
+        build_and_load_data(st.session_state["selected_dataset"])
+        st.info(f"{selection_type} Selected: {selected_file}")
+
+        # if "Folder" in selection_type:
+
+        #     selected_folder_files = [f for f in os.listdir(st.session_state["selected_dataset"]) if os.path.isfile(os.path.join(st.session_state["selected_dataset"], f))]
+        #     view_selected_folder_files = st.selectbox("Choose a file:", selected_folder_files)
+
+        # files = [
+        #     f
+        #     for f in os.listdir(upload_folder)
+        #     if os.path.isfile(os.path.join(upload_folder, f))
+        # ]
+        # st.write(files)
+        # if files:
+        #     selected_file = st.selectbox("Select a previously uploaded file:", files)
+        #     st.session_state["selected_dataset"] = selected_file
+        #     st.info(f"You selected {selected_file}")
+        #     build_and_load_data(upload_folder)
+        #     # previewVisualization(st.session_state["cells_list"])
+        # else:
+        #     st.warning("No files found in the directory!")
     else:
         st.warning("No files have been uploaded yet.")
 
 
+if st.session_state.cells_list == True:
+    st.warning("Please upload a zipped file of ROIs or a CSV/TXT file.")
+    st.stop()
+
+
 st.markdown("## Preview of Cell Data")
 
 st.warning(
     "⚠️ This is a preview your uploaded raw data. We have not preprocessed your data yet to close the curves and remove duplicates. Please continue to the next page to preprocess your data."
 )
 
+(
+    col1,
+    col2,
+) = st.columns(2)
+
+
 # Sanity check visualization
 cell_num = st.number_input(
     f"Visualize a cell. Pick a number between 0 and {len(st.session_state.cells_list)-1}",
@@ -201,7 +244,7 @@ def handle_uploaded_file(uploaded_file, destination_folder):
 )  # Using a constant value for z, placing the line on the "floor" of the 3D space
 
 # Define a custom color for the line plot
-line_color = "rgb(31, 119, 180)"  # Adjust the RGB values as per your preference
+line_color = "rgb(255, 0, 191)"  # Adjust the RGB values as per your preference
 
 # Create a 3D trace for the cell data
 trace = go.Scatter3d(

cells/streamlit/cellgeometry/utils/basic.py

@@ -11,6 +11,16 @@ def perimeter(xy):
     xy : array-like, shape=[n_points, 2]
         Polygon, such that:
         x = xy[:, 0]; y = xy[:, 1]
+
+    Examples
+    --------
+    >>> import numpy as np
+    >>> xy = np.array([[0, 0], [0, 1], [1, 1], [1, 0]])
+    >>> np.isclose(perimeter(xy), 4.0)
+    True
+    >>> xy = np.array([[0, 0], [0, 3], [4, 3], [4, 0]])
+    >>> np.isclose(perimeter(xy), 14.0)
+    True
     """
     first_point = gs.expand_dims(gs.array(xy[0]), axis=0)
     xy1 = gs.concatenate([xy[1:], first_point], axis=0)

cells/streamlit/cellgeometry/utils/data_utils.py

@@ -227,3 +227,36 @@ def parse_coordinates(file_path):
         coordinates[cell_id] = np.array(cell_data)
 
     return coordinates
+
+
+def get_file_or_folder_type(path):
+    """Determine whether a given path points to a file, a folder, or neither.
+
+    Parameters
+    ----------
+    path : str
+        The path to the item (file or folder) you want to check.
+
+    Returns
+    -------
+    str
+        A string indicating the type of the item:
+        - 'File' if the path points to a file.
+        - 'Folder' if the path points to a folder.
+        - 'Neither' if the path does not point to a file or folder.
+
+    Examples
+    --------
+    >>> get_file_or_folder_type('/path/to/your/selected/file_or_folder')
+    'Folder'
+    >>> get_file_or_folder_type('/path/to/your/selected/example.txt')
+    'File'
+    >>> get_file_or_folder_type('/path/to/nonexistent/item')
+    'Neither'
+    """
+    if os.path.isfile(path):
+        return ":page_facing_up: File"
+    elif os.path.isdir(path):
+        return ":file_folder: Folder"
+    else:
+        return "Neither"

tests/test_basic.py → cells/streamlit/tests/test_basic.py

@@ -1,6 +1,6 @@
 """Unit tests for the basic shape features."""
 
-import dyn.features.basic as basic
+import cells.streamlit.cellgeometry.utils.basic as basic
 import geomstats.backend as gs