Add summary of changes to MetricComputation.md

This markdown file summarizes changes made to Metric_computation.py, including significant logic updates such as the removal of migration time calculations and restoration of gene-specific metrics.

Author: smishra3

EMT_data_analysis/tracking_Aug2024/MetricComputation.md

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+# Summary of Changes to Metric_computation.py Since Sept 2024
+
+  Timeline of Changes
+
+  | Date       | Commit  | Summary                                  |
+  |------------|---------|------------------------------------------|
+  | 2025-04-07 | fdc6a0c | Added import_folder() function           |
+  | 2025-04-11 | bfa002a | Bugfix                                   |
+  | 2025-04-14 | e25cb77 | Path updates                             |
+  | 2025-04-29 | 77d8cab | Processing resubmission data             |
+  | 2025-05-14 | 906998e | Batch processing scripts                 |
+  | 2025-07-30 | 6fc7597 | Restored to using Quilt data             |
+  | 2025-08-21 | 61904ba | Column name updates (Movie ID → Data ID) |
+  | 2025-08-25 | 91db0e9 | Removed unused metric column             |
+
+  ---
+  Major Changes Analysis
+
+  1. IO Changes (Not Breaking)
+
+  - Movie ID → Data ID column name changes throughout
+  - Restored io.load_bf_colony_features() and io.load_imaging_and_segmentation_dataset() instead of CSV file loading
+  - Removed temporary import_folder() function
+
+  2. LOGIC CHANGE: Migration Time Calculation REMOVED ⚠️
+
+  Before (April 2025):
+  ```
+  # In add_bottom_mip_migration():
+  raw_values = df_area['Area at the glass (pixels)'].values
+  df_area['dy2'] = savgol_filter(raw_values, polyorder=2, window_length=40, deriv=2)
+  d_filt = df_area[(df_area.Timepoint>=35) & (df_area.Timepoint<=80)]
+  index_infl = d_filt['dy2'].idxmax()
+  x_p = df_area['Timepoint'][index_infl]
+  df_area['Migration time (h)'] = x_p * (30/60)
+  ```
+
+  After (August 2025): This entire migration time calculation was REMOVED.
+
+  Impact: The Migration time (h) column is no longer computed in add_bottom_mip_migration(). This is a significant 
+  logic removal.
+
+  3. LOGIC CHANGE: Gene Metrics Restored ✓
+
+  Before (April 2025): Gene-specific metrics were commented out:
+  ```
+  # ######--computing Time of max EOMES expression ------ #####
+  # df_eomes=df_int[(df_int.Gene=='EOMES|TBR2') | (df_int.Gene=='TBR2|EOMES')]
+  # ... (all commented)
+  ```
+
+  After (July 2025): Gene metrics were restored and expanded:
+  - Time of max EOMES expression
+  - Time of max TBXT expression (NEW)
+  - Time of inflection of E-cad expression
+  - Time of half-maximal SOX2 expression
+
+  4. Output Column Removal
+
+  Removed from final output (August 2025):
+  ```
+  # Removed: 'Time of max expression (h)'
+  ```
+  This column was removed from the final feature list.
+
+  ---
+  #Summary Table
+
+  | Change                                         | Type   | Impact  |
+  |------------------------------------------------|--------|------------------------------------------------------------|
+  | Movie ID → Data ID                             | IO     | Not breaking   |
+  | Quilt data loading restored                    | IO     | Not breaking  |
+  | Migration time calculation REMOVED             | LOGIC  | Breaking - metric no longer computed  |
+  | Gene-specific metrics RESTORED                 | LOGIC  | Significant - EOMES, TBXT, CDH1, SOX2 metrics now computed |
+  | Time of max expression (h) removed from output | Output | Minor - column removed   |
+  | import_folder() removed                        | IO     | Not breaking (was temporary)  |
+  ---
+  Conclusion
+
+  Two significant logic changes:
+
+  1. Migration time calculation REMOVED from add_bottom_mip_migration() - this metric based on second derivative of
+  area at glass is no longer computed
+  2. Gene-specific metrics RESTORED - Time of max EOMES, TBXT expression, E-cad inflection, and SOX2 half-maximal are
+  now computed (were commented out before)
+
+  The migration time removal could be significant if downstream analysis depended on that metric.
+