Feature/pip support

src/midrc_react/core/jsdcontroller.py

@@ -324,6 +324,9 @@ def build_date_list(df1, df2):
                 str_col = category[:-6]
                 num_col = data_source_1.numeric_cols[str_col]['raw column']
 
+                # remove the 'Not Reported' data before calculation
+                combined_df = combined_df[pd.to_numeric(combined_df[num_col], errors='coerce').notnull()]
+
                 input_data = [float(calc_ks2_samp_by_feature(combined_df[combined_df['date'] <= date],
                                                              num_col)['Dataset 0 vs Dataset 1']) for date in date_list]
 

src/midrc_react/gui/pyside6/grabbablewidget.py

@@ -49,6 +49,7 @@ def __init__(self, parent: QWidget = None, save_file_prefix: str = DEFAULT_SAVE_
         """
         self.save_dialog_open = False  # Indicates if the save dialog is currently open
         super().__init__(parent)
+        self.copyable_data: str | None = None  # new attribute for copyable text data
         self.save_file_prefix = save_file_prefix
         parent.setContextMenuPolicy(Qt.CustomContextMenu)
         parent.customContextMenuRequested.connect(self.show_context_menu)
@@ -82,8 +83,13 @@ def show_context_menu(self, pos):
             None
         """
         context_menu = QMenu(self.parent)
-        copy_action = QAction("Copy", self.parent)
-        save_action = QAction("Save", self.parent)
+        # New action: Copy Data, enabled only if copyable_data is set
+        copy_data_action = QAction("Copy Data", self.parent)
+        copy_data_action.setEnabled(bool(self.copyable_data))
+        copy_data_action.triggered.connect(self.copy_data_to_clipboard)
+        context_menu.addAction(copy_data_action)
+        copy_action = QAction("Copy Image", self.parent)
+        save_action = QAction("Save Image", self.parent)
 
         copy_action.triggered.connect(self.copy_to_clipboard)
         save_action.triggered.connect(self.save_to_disk)
@@ -93,7 +99,7 @@ def show_context_menu(self, pos):
 
         # Only display this action if we don't have the high-res save dialog open for this widget
         if not self.save_dialog_open:
-            save_high_res_action = QAction("Save High Resolution", self.parent)
+            save_high_res_action = QAction("Save High Resolution Image", self.parent)
             save_high_res_action.triggered.connect(self.save_high_res_to_disk)
             context_menu.addAction(save_high_res_action)
 
@@ -190,6 +196,14 @@ def save_high_res_to_disk(self) -> None:
 
         self.save_dialog_open = False
 
+    def copy_data_to_clipboard(self):
+        """
+        Copy the stored copyable_data text to the clipboard.
+        """
+        if self.copyable_data:
+            clipboard = QApplication.clipboard()
+            clipboard.setText(self.copyable_data)
+
 
 class SaveWidgetAsImageDialog(QDialog):
     """
@@ -366,3 +380,4 @@ def save_chart_to_disk(self):
             None
         """
         self.grabbable_mixin.save_to_disk()
+

src/midrc_react/gui/pyside6/jsdview.py

@@ -289,6 +289,7 @@ def add_spider_chart_view(self) -> GrabbableChartView:
             self.spider_chart, save_file_prefix="MIDRC-REACT_spider_chart",
         )
         self.spider_chart_vbox.addWidget(spider_chart_view)
+        self.spider_chart_view = spider_chart_view  # store reference for copyable data
         return spider_chart_view
 
     def update_pie_chart_dock(self, sheet_dict: Dict[Any, Any]) -> None:
@@ -384,6 +385,26 @@ def _create_pie_chart_series(series: QPieSeries, category: str) -> GrabbableChar
         chart.legend().setAlignment(Qt.AlignRight)
         return chart_view
 
+    def _set_spider_chart_copyable_data(self, spider_plot_values_dict: Dict[Any, Dict[str, float]]) -> None:
+        """
+        Set the copyable data for the spider chart.
+
+        Args:
+            spider_plot_values_dict (dict): Dictionary containing series values keyed by index pairs.
+
+        Returns:
+            None
+        """
+        if hasattr(self, 'spider_chart_view') and spider_plot_values_dict:
+            headers = sorted(next(iter(spider_plot_values_dict.values())).keys())
+            formatted_text = "File 1\tFile 2\t" + "\t".join(headers) + "\n"
+            for series_key, series in spider_plot_values_dict.items():
+                file1 = self._dataselectiongroupbox.file_comboboxes[series_key[0]].currentText()
+                file2 = self._dataselectiongroupbox.file_comboboxes[series_key[1]].currentText()
+                values = "\t".join(str(series[label]) for label in headers)
+                formatted_text += f"{file1}\t{file2}\t{values}\n"
+            self.spider_chart_view.grabbable_mixin.copyable_data = formatted_text
+
     def update_spider_chart(self, spider_plot_values_dict: Dict[Any, Dict[str, float]]) -> bool:
         """
         Update the spider chart with the provided plot values.
@@ -397,6 +418,8 @@ def update_spider_chart(self, spider_plot_values_dict: Dict[Any, Dict[str, float
         if not spider_plot_values_dict:
             return False
 
+        self._set_spider_chart_copyable_data(spider_plot_values_dict)
+
         self.spider_chart.removeAllSeries()
         for axis in self.spider_chart.axes():
             self.spider_chart.removeAxis(axis)
@@ -570,7 +593,7 @@ def update_jsd_timeline_plot(self, jsd_model) -> bool:
         for c, column_info in enumerate(jsd_model.column_infos):
             col: int = c * 2
             series: QLineSeries = QLineSeries()
-            series.setName(f"{column_info['file1']} vs {column_info['file2']} {column_info['category']} JSD")
+            series.setName(f"{column_info['file1']} vs {column_info['file2']} {column_info['category']} Distance")
             row_count: int = jsd_model.rowCount(jsd_model.createIndex(0, col))
             for i in range(row_count):
                 time_point: Optional[float] = convert_date_to_milliseconds(jsd_model.input_data[col][i])
@@ -712,3 +735,6 @@ def clear_layout(layout: Optional[QLayout]) -> bool:
         layout.removeItem(child)
 
     return True
+
+
+

src/midrc_react/plugins/missing_date_plugin.py

@@ -0,0 +1,33 @@
+#  Copyright (c) 2025 Medical Imaging and Data Resource Center (MIDRC).
+#
+#      Licensed under the Apache License, Version 2.0 (the "License");
+#      you may not use this file except in compliance with the License.
+#      You may obtain a copy of the License at
+#
+#         http://www.apache.org/licenses/LICENSE-2.0
+#
+#      Unless required by applicable law or agreed to in writing, software
+#      distributed under the License is distributed on an "AS IS" BASIS,
+#      WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+#      See the License for the specific language governing permissions and
+#      limitations under the License.
+#
+
+"""
+This module contains functions for processing TSV files downloaded from the data.MIDRC.org website.
+"""
+
+from datetime import datetime
+import re
+
+import pandas as pd
+
+def process_dataframe(df):
+    """Applies both transformations on a pandas DataFrame."""
+    df['date'] = pd.to_datetime(datetime.today().date())
+    return df
+
+def preprocess_data(df):
+    """Preprocesses a pandas DataFrame."""
+    return process_dataframe(df)
+