37 resserved keyword filepath overwritten by nexus field

src/hdfmap/__init__.py

@@ -66,8 +66,8 @@
     'set_all_logging_level', 'version_info', 'module_info'
 ]
 
-__version__ = "1.1.0"
-__date__ = "2025/10/27"
+__version__ = "1.1.1"
+__date__ = "2025/11/17"
 __author__ = "Dan Porter"
 
 

src/hdfmap/eval_functions.py

@@ -254,6 +254,7 @@ def select_ids(startswith=''):
             if symbol.startswith(startswith) and hdf_namespace.get(name := symbol[len(startswith):], '') in hdf_file
         )
 
+    extra_data = extra_hdf_data(hdf_file)
     namespace = {symbol: dataset2data(hdf_file[hdf_namespace[name]]) for symbol, name in select_ids()}
     strings = {symbol: dataset2str(hdf_file[hdf_namespace[name]], units=True) for symbol, name in select_ids('s_')}
     datasets = {symbol: hdf_file[hdf_namespace[name]] for symbol, name in select_ids('d_')}
@@ -266,8 +267,8 @@ def select_ids(startswith=''):
         if name not in data_namespace and name not in GLOBALS_NAMELIST
            and hdf_namespace.get(name, '') not in hdf_file
     }
-    # combine with precendence
-    data = {**defaults, **hdf_paths, **hdf_names, **datasets, **strings, **namespace}
+    # combine with precedence
+    data = {**defaults, **hdf_paths, **hdf_names, **datasets, **strings, **namespace, **extra_data}
     # add or overwrite data in data_namespace
     data_namespace.update(data)
     return data
@@ -304,16 +305,13 @@ def prepare_expression(hdf_file: h5py.File, expression: str, hdf_namespace: dict
     """
     if data_namespace is None:
         data_namespace = {}
-    # get extra data
-    extra_data = extra_hdf_data(hdf_file)
     # find name@attribute in expression
     attributes = {
         f"attr__{name}_{attr}": dataset_attribute(hdf_file[path], attr)
-        for name, attr in re_dataset_attributes.findall(expression)
+        for name, attr in re_dataset_attributes.findall(expression)  # name@attr
         if (path := hdf_namespace.get(name, '')) in hdf_file
     }
-    extra_data.update(attributes)
-    data_namespace.update(extra_data)  # update in the parent function
+    data_namespace.update(attributes)  # adds data in the parent function
     # replace name@attribute in expression
     expression = re_dataset_attributes.sub(r'attr__\g<1>_\g<2>', expression)
     # find values with defaults '..?(..)'

src/hdfmap/hdfmap_class.py

@@ -356,7 +356,7 @@ def add_roi(self, name: str, cen_i: int | str, cen_j: int | str,
             *name*_mean -> returns the mean of each image in the ROI array
             *name*_bkg -> returns the background ROI array (area around ROI)
             *name*_rmbkg -> returns the total with background subtracted
-            *name*_box -> returns the pixel positions of the ROI
+            *name*_box -> returns the pixel positions of the ROI corners
             *name*_bkg_box -> returns the pixel positions of the background ROI
 
         :param name: string name of the ROI

src/hdfmap/nexus.py

@@ -28,6 +28,7 @@
 NX_DETECTOR = 'NXdetector'
 NX_DETECTOR_DATA = 'data'
 NX_IMAGE_DATA = 'image_data'
+NX_IMAGE_NUMBER = 'path'
 NX_UNITS = 'units'
 logger = create_logger(__name__)
 
@@ -189,6 +190,7 @@ class NexusMap(HdfMap):
         nxmap.populate(nxs, default_entry_only=True)  # populates only from the default entry
 
     # Special behaviour
+    nxmap.image_data is preferentially populated by NXdetector groups
     nxmap['axes'] -> return path of default axes dataset
     nxmap['signal'] -> return path of default signal dataset
     nxmap['image_data'] -> return path of first area detector data object
@@ -340,6 +342,7 @@ def generate_image_data_from_nxdetector(self):
             # detector data is stored in NXdata in dataset 'data'
             data_path = build_hdf_path(group_path, NX_DETECTOR_DATA)
             image_data_path = build_hdf_path(group_path, NX_IMAGE_DATA)
+            image_data_numbers = build_hdf_path(group_path, NX_IMAGE_NUMBER)
             logger.debug(f"Looking for image_data at: '{data_path}' or '{image_data_path}'")
             if data_path in self.datasets and is_image(self.datasets[data_path].shape, image_ndim):
                 logger.info(f"Adding image_data ['{detector_name}'] = '{data_path}'")
@@ -348,13 +351,22 @@ def generate_image_data_from_nxdetector(self):
                 # also save image_data if available
                 if image_data_path in self.datasets:
                     detector_name = f"{detector_name}_image_list"
-                    logger.info(f"Adding image_data ['{detector_name}'] = '{image_data_path}'")
+                    logger.info(f"Adding image_data str ['{detector_name}'] = '{image_data_path}'")
                     self.image_data[detector_name] = image_data_path
                     self.arrays[detector_name] = image_data_path
+                elif image_data_numbers in self.datasets:
+                    detector_name = f"{detector_name}_image_list"
+                    logger.info(f"Adding image_data 1D ['{detector_name}'] = '{image_data_numbers}'")
+                    self.image_data[detector_name] = image_data_numbers
+                    self.arrays[detector_name] = image_data_numbers
             elif image_data_path in self.datasets:
-                logger.info(f"Adding image_data ['{detector_name}'] = '{image_data_path}'")
+                logger.info(f"Adding image_data str ['{detector_name}'] = '{image_data_path}'")
                 self.image_data[detector_name] = image_data_path
                 self.arrays[detector_name] = image_data_path
+            elif image_data_numbers in self.datasets:
+                logger.info(f"Adding image_data 1D ['{detector_name}'] = '{image_data_numbers}'")
+                self.image_data[detector_name] = image_data_numbers
+                self.arrays[detector_name] = image_data_numbers
             else:
                 # Use first dataset with > 2 dimensions
                 image_dataset = next((

tests/create_test_files.py

@@ -17,6 +17,7 @@
     (DIR + 'i16/982681.nxs', 'i16 pil2m single point scan'),
     (DIR + 'i16/928878.nxs', 'i16 merlin 2d delta gam calibration'),
     (DIR + 'i16/1109527.nxs', 'i16 pilatus eta scan, new nexus format'),
+    (DIR + 'i16/1113658.nxs', 'i16 bpm scan, new nexus format'),
     (DIR + 'i16/processed/1090391_msmapper.nxs', 'msmapper volume'),
     (DIR + 'i10/i10-608314.nxs', 'i10 pimte scan'),
     (DIR + 'i10/i10-618365.nxs', 'i10 scan'),

tests/test_edge_cases.py

@@ -18,6 +18,7 @@ def test_edge_cases():
         assert path.isfile(chk['filename']) is True, f"{chk['filename']} doesn't exist"
         mymap = hdfmap.create_nexus_map(chk['filename'])
         assert isinstance(mymap, hdfmap.NexusMap), f"{chk['filename']} is not NexusMap"
+        assert mymap('filepath') == chk['filename']
         assert len(mymap.combined) == chk['len_combined'], "{chk['filename']} has wrong size of combined"
         assert len(mymap.scannables) == chk['len_scannables'], f"{chk['filename']} has wrong size of scannables"
         assert mymap.scannables_length() == chk['scannables_length'], f"{chk['filename']} has wrong scannables_length"
@@ -53,6 +54,34 @@ def test_new_i16_file():
     assert fname == '1040323.nxs'
 
 
+@only_dls_file_system
+def test_newer_i16_file():
+    filename = '/dls/science/groups/das/ExampleData/hdfmap_tests/i16/1109527.nxs'
+    assert path.isfile(filename) is True, f"{filename} doesn't exist"
+    mymap = hdfmap.create_nexus_map(filename)
+    with hdfmap.hdf_loader.load_hdf(filename) as hdf:
+        axes, signal, IMAGE, fname, fpath = mymap.eval(hdf, 'axes, signal, _IMAGE, filename, filepath')
+    assert axes.shape == (61, ), 'expression "axes" has wrong shape'
+    assert signal.shape == (61,), 'expression "axes" has wrong shape'
+    assert signal.max() == 692919
+    assert isinstance(fname, str), "expression 'filename' has wrong type"
+    assert filename.endswith(fname)
+    assert isinstance(fpath, str), "expression 'filepath' has wrong type"
+    assert fpath == filename
+
+
+@only_dls_file_system
+def test_i16_bpm_file():
+    filename = '/dls/science/groups/das/ExampleData/hdfmap_tests/i16/1113658.nxs'
+    assert path.isfile(filename) is True, f"{filename} doesn't exist"
+    mymap = hdfmap.create_nexus_map(filename)
+    assert mymap.get_image_path() == '/entry/instrument/bpm/path'
+    with hdfmap.hdf_loader.load_hdf(filename) as hdf:
+        image = mymap.get_image(hdf)
+    assert image.ndim == 0, 'bpm image has wrong shape'
+    assert int(image) == 11, 'bpm image has wrong value'
+
+
 @only_dls_file_system
 def test_msmapper_file():
     filename = '/dls/science/groups/das/ExampleData/hdfmap_tests/i16/processed/1098101_msmapper.nxs'