feat: Beckman Vi-Cell XR - Add unread data (#1044)

Update for this ticket:
[BNCH-115074](https://jira.benchling.team/browse/BNCH-115074)

---------

Co-authored-by: Nathan Stender <nathan.stender@benchling.com>

Author: felipenarv

src/allotropy/allotrope/converter.py

@@ -103,6 +103,7 @@
     "$": "_DOLLAR_",
     "~": "_TILDE_",
     "?": "_QMARK_",
+    "^": "_CARET_",
     # NOTE: this MUST be at the end, or it will break other key replacements.
     " ": "_",
 }

src/allotropy/parsers/beckman_vi_cell_xr/vi_cell_xr_structure.py

@@ -30,6 +30,17 @@ def create_measurement_group(data: SeriesData) -> MeasurementGroup:
         viable_cell_count if viable_cell_count is None else round(viable_cell_count)
     )
 
+    custom_info_measurement_group = data.get_custom_keys(
+        {
+            "experimental data identifier": ["File Name", "File name"],
+            "log date": ["LogDate", "Log date"],
+            "file date": ["FileDate", "File date"],
+        }
+    )
+
+    # Mark unused keys to be ignored
+    data.mark_read({"Settings:", "Results:", "Settings", "Results"})
+
     return MeasurementGroup(
         analyst=DEFAULT_ANALYST,
         measurements=[
@@ -45,9 +56,70 @@ def create_measurement_group(data: SeriesData) -> MeasurementGroup:
                 total_cell_density=data.get(float, "Total cells/ml (x10^6)"),
                 average_total_cell_diameter=data.get(float, "Avg. diam. (microns)"),
                 viable_cell_count=viable_cell_count,
+                dead_cell_count=data.get(float, "Nonviable cells"),
                 average_total_cell_circularity=data.get(float, "Avg. circ."),
+                maximum_cell_diameter_setting=data.get(float, "Max diam. (microns)")
+                or data.get(float, "Maximum diameter (microns)"),
+                minimum_cell_diameter_setting=data.get(float, "Min diam. (microns)")
+                or data.get(float, "Minimum diameter (microns)"),
+                sample_custom_info=data.get_custom_keys(
+                    {
+                        "Internal Dilution",
+                        "Dilution",
+                    }
+                ),
+                device_control_custom_info=data.get_custom_keys(
+                    {
+                        "Aspirate cycles",
+                        "Probe volume (ml x 10^-6)",
+                        "Trypan blue mixing cycles",
+                    }
+                ),
+                data_processing_custom_info=data.get_custom_keys(
+                    {
+                        "Decluster degree",
+                        "Viable cell spot area (%)",
+                        "Viable spot area",
+                        "Viable cell spot brightness (%)",
+                        "V. cell spot brightness (%)",
+                        "Cell sharpness",
+                        "Sharpness",
+                        "Cell brightness (%)",
+                        "Brightness (%)",
+                        "Brightness",
+                        "Analysis version",
+                        "Number of bins",
+                        "Minimum circularity",
+                        "Sample depth (microns)",
+                    }
+                ),
+                image_processing_custom_info=data.get_custom_keys(
+                    {
+                        "Images",
+                        "Saved images",
+                        "ImageBaseName",
+                        "Frames",
+                        "Microns/pixel ratio",
+                        "ImageDirectory",
+                        "Image size",
+                        "Field of view (microns)",
+                    }
+                ),
+                processed_data_custom_info=data.get_custom_keys(
+                    {
+                        "Avg. cells / image",
+                        "Average cells / image",
+                        "Background intensity sum",
+                        "Total diameter sum",
+                        "Total circularity sum",
+                        "Avg. background intensity",
+                        "Avg. bg intensity",
+                    }
+                ),
+                custom_info=data.get_unread(),
             )
         ],
+        custom_info=custom_info_measurement_group,
     )
 
 

src/allotropy/parsers/utils/pandas.py

@@ -287,6 +287,29 @@ def _get_matching_keys(self, key_or_keys: str | set[str]) -> set[str]:
         }
 
     def get_custom_keys(
+        self, key_or_keys: str | set[str] | dict[str, list[str]]
+    ) -> dict[str, float | str | None]:
+        if isinstance(key_or_keys, dict):
+            return self._get_custom_keys_from_dict(key_or_keys)
+        return self._get_custom_keys_from_str_or_set(key_or_keys)
+
+    def _get_custom_keys_from_dict(
+        self, key_or_keys: dict[str, list[str]]
+    ) -> dict[str, float | str | None]:
+        if isinstance(key_or_keys, dict):
+            result = {}
+            for output_key, candidate_keys in key_or_keys.items():
+                for candidate_key in candidate_keys:
+                    value = self._validate_raw(
+                        self._get_custom_key(candidate_key), SeriesData.NOT_NAN
+                    )
+                    if value is not None:
+                        result[output_key] = value
+                        break  # Stop iteration once a value is found
+                # If no value was found for any candidate key, the output_key is excluded
+            return result
+
+    def _get_custom_keys_from_str_or_set(
         self, key_or_keys: str | set[str]
     ) -> dict[str, float | str | None]:
         return {