Merge pull request #779 from borondics/SoftiMax_reader

[ENH] SoftiMax HDF5 reader
Quasars · Dec 18, 2024 · 2bbb856 · 2bbb856
2 parents 0d49e68 + fbf168a
commit 2bbb856
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Showing 3 changed files with 33 additions and 12 deletions.
diff --git a/orangecontrib/spectroscopy/io/__init__.py b/orangecontrib/spectroscopy/io/__init__.py
@@ -21,6 +21,6 @@
 
 # Facility-specific readers
 from .diamond import NXS_STXM_Diamond_I08
-from .maxiv import HDRReader_STXM
+from .maxiv import HDRReader_STXM, HDF5Reader_SoftiMAX
 from .soleil import SelectColumnReader, HDF5Reader_HERMES, HDF5Reader_ROCK
 from .cls import HDF5Reader_SGM
diff --git a/orangecontrib/spectroscopy/io/maxiv.py b/orangecontrib/spectroscopy/io/maxiv.py
@@ -4,6 +4,7 @@
 from Orange.data import FileFormat
 
 from orangecontrib.spectroscopy.io.util import SpectralFileFormat, _spectra_from_image
+from orangecontrib.spectroscopy.io.soleil import HDF5Reader_HERMES
 
 
 class HDRReader_STXM(FileFormat, SpectralFileFormat):
@@ -105,4 +106,24 @@ def read_spectra(self):
         x_loc = axes[1]['Points']
         y_loc = axes[0]['Points']
         features = np.asarray(axes[2]['Points'])
-        return _spectra_from_image(spectra, features, x_loc, y_loc)
+        return _spectra_from_image(spectra, features, x_loc, y_loc)
+
+
+class HDF5Reader_SoftiMAX(FileFormat, SpectralFileFormat):
+    """ A very case specific reader for HDF5 files from the SoftiMAX beamline in MAX-IV"""
+    EXTENSIONS = ('.hdf5',)
+    DESCRIPTION = 'HDF5 file @SoftiMAX/MAX-IV'
+    PRIORITY = HDF5Reader_HERMES.PRIORITY + 1
+
+    def read_spectra(self):
+        import h5py
+        with h5py.File(self.filename, 'r') as hdf5_file:
+            if 'entry1/collection/beamline' in hdf5_file and \
+                    hdf5_file['entry1/collection/beamline'][()].astype('str') == ['SLS Sophie at Softimax MAXIV']:
+                x_locs = np.array(hdf5_file['entry1/counter0/sample_x'])
+                y_locs = np.array(hdf5_file['entry1/counter0/sample_y'])
+                energy = np.array(hdf5_file['entry1/counter0/energy'])
+                intensities = np.array(hdf5_file['entry1/counter0/data']).T
+                return _spectra_from_image(intensities, energy, y_locs, x_locs)
+            else:
+                raise IOError("Not a SoftiMAX file")
diff --git a/orangecontrib/spectroscopy/io/soleil.py b/orangecontrib/spectroscopy/io/soleil.py
@@ -43,16 +43,16 @@ class HDF5Reader_HERMES(FileFormat, SpectralFileFormat):
 
     def read_spectra(self):
         import h5py
-        hdf5_file = h5py.File(self.filename)
-        if 'entry1/collection/beamline' in hdf5_file and \
-                hdf5_file['entry1/collection/beamline'][()].astype('str') == 'Hermes':
-            x_locs = np.array(hdf5_file['entry1/Counter0/sample_x'])
-            y_locs = np.array(hdf5_file['entry1/Counter0/sample_y'])
-            energy = np.array(hdf5_file['entry1/Counter0/energy'])
-            intensities = np.array(hdf5_file['entry1/Counter0/data']).T
-            return _spectra_from_image(intensities, energy, x_locs, y_locs)
-        else:
-            raise IOError("Not an HDF5 HERMES file")
+        with h5py.File(self.filename, 'r') as hdf5_file:
+            if 'entry1/collection/beamline' in hdf5_file and \
+                    hdf5_file['entry1/collection/beamline'][()].astype('str') == 'Hermes':
+                x_locs = np.array(hdf5_file['entry1/Counter0/sample_x'])
+                y_locs = np.array(hdf5_file['entry1/Counter0/sample_y'])
+                energy = np.array(hdf5_file['entry1/Counter0/energy'])
+                intensities = np.array(hdf5_file['entry1/Counter0/data']).T
+                return _spectra_from_image(intensities, energy, x_locs, y_locs)
+            else:
+                raise IOError("Not an HDF5 HERMES file")
 
 
 class HDF5Reader_ROCK(FileFormat, SpectralFileFormat):