- Added function load_monitor_log.

- Added JSON config to use Monitor Normalisation - Improved error messages for missing related filename groups or log files.
mantidproject · Jun 4, 2024 · 16973ff · 16973ff
1 parent 619bdd4
commit 16973ff
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Showing 2 changed files with 52 additions and 19 deletions.
diff --git a/scripts/operations_tests/operations_tests.py b/scripts/operations_tests/operations_tests.py
@@ -19,6 +19,7 @@
 
 import numpy as np
 import pandas as pd
+
 try:
     from plotly import graph_objs as go
     from plotly.subplots import make_subplots
@@ -28,6 +29,7 @@
     exit(1)
 
 sys.path.append(str(Path(__file__).resolve().parent.parent.parent))
+from mantidimaging.core.utility.data_containers import FILE_TYPES
 from mantidimaging.core.io.filenames import FilenameGroup  # noqa: E402
 from mantidimaging.core.io.loader import loader  # noqa: E402
 from mantidimaging.core.operations.loader import load_filter_packages  # noqa: E402
@@ -139,8 +141,13 @@ def run_tests(self):
     def run_test(self, test_case):
         image_stack = self.load_image_stack()
 
+        # Handling various pre-run steps
         if test_case.pre_run_step == 'add_nan':
-            self.image_stack = self.add_nan(image_stack, fraction=0.1)
+            image_stack = self.add_nan(image_stack, fraction=0.1)
+        elif test_case.pre_run_step == 'add_flats_and_darks':
+            self.add_flats_and_darks(test_case.params)
+        elif test_case.pre_run_step == 'load_monitor_log':
+            self.load_monitor_log(test_case.params)
 
         test_case.duration, new_image_stack = self.time_operation(image_stack, test_case.op_func, test_case.params)
         file_name = config_manager.save_dir / (test_case.test_name + ".npz")
@@ -163,6 +170,34 @@ def run_test(self, test_case):
 
         TEST_CASE_RESULTS.append(test_case)
 
+    def load_monitor_log(self, params):
+        filename_group = FilenameGroup.from_file(config_manager.load_sample)
+        log_file_type = params['log_file_type']
+
+        if not hasattr(FILE_TYPES, log_file_type):
+            raise AttributeError(f"{log_file_type} not found in FILE_TYPES")
+
+        print(f"Looking for related files of type: {log_file_type}")
+        file_type_enum = getattr(FILE_TYPES, log_file_type)
+        related_filename_group = filename_group.find_related(file_type_enum)
+
+        if not related_filename_group:
+            raise FileNotFoundError(f"Related filename group for {log_file_type} not found.")
+
+        print(f"Related filename group found: {related_filename_group}")
+        related_filename_group.find_all_files()
+
+        log_file_path = filename_group.find_log_file()
+        if not log_file_path:
+            raise FileNotFoundError("Log file not found.")
+
+        print(f"Log file path: {log_file_path}")  # Debug statement
+
+        with open(log_file_path) as file:
+            log_data = file.read()
+            print(f"Loaded monitor log from {log_file_path}")
+            return log_data
+
     def add_nan(self, image_stack, fraction=0.001):
         data = image_stack.data
         total_elements = data.size

diff --git a/scripts/operations_tests/test_cases.json b/scripts/operations_tests/test_cases.json
@@ -642,39 +642,37 @@
       }
     ]
   },
-  "Circular Mask": {
+  "Monitor Normalisation": {
     "params": {
-      "circular_mask_ratio": 0.95,
-      "circular_mask_value": 0.0
+      "use_dark": false,
+      "selected_normalisation": "Monitor"
     },
-    "source_data": "reconstructedSlices",
+    "source_data": "flower128",
     "cases": [
       {
-        "test_name": "circular_mask_default",
+        "test_name": "default_normalisation",
+        "pre_run_step": "load_monitor_log",
         "params": {
-          "circular_mask_ratio": 0.95,
-          "circular_mask_value": 0.0
+          "log_file_type": "SAMPLE_LOG"
         }
       },
       {
-        "test_name": "circular_mask_tight",
-        "params": {
-          "circular_mask_ratio": 0.5,
-          "circular_mask_value": 0.0
-        }
+        "test_name": "no_log_file",
+        "pre_run_step": "none",
+        "params": {}
       },
       {
-        "test_name": "circular_mask_loose",
+        "test_name": "incorrect_log_values",
+        "pre_run_step": "load_monitor_log",
         "params": {
-          "circular_mask_ratio": 0.99,
-          "circular_mask_value": 0.0
+          "log_file_type": "FLAT_BEFORE_LOG"
         }
       },
       {
-        "test_name": "circular_mask_value",
+        "test_name": "different_exposure_times",
+        "pre_run_step": "load_monitor_log",
         "params": {
-          "circular_mask_ratio": 0.95,
-          "circular_mask_value": -1000
+          "log_file_type": "FLAT_AFTER_LOG"
         }
       }
     ]