[HDF5Scan] first raw add of the `christian` hdf5/nexus file for tomography

tomoscan/esrf/hdf5scan.py

@@ -37,6 +37,7 @@ import numpy
 from silx.io.url import DataUrl
 from silx.utils.enum import Enum as _Enum
 from tomoscan.utils import docstring
+from silx.io.utils import get_data
 import logging
 import typing
 
@@ -312,9 +313,7 @@ class HDF5TomoScan(TomoScanBase):
         """
         if self._tomo_n is None and self.master_file and os.path.exists(self.master_file):
             if self.projections:
-                filter_fct = lambda x: x.is_return is False
-                none_returnproj_frames = list(filter(filter_fct, self.projections))
-                return len(none_returnproj_frames)
+                return len(self.projections)
             else:
                 return None
         else:
@@ -388,17 +387,17 @@ class HDF5TomoScan(TomoScanBase):
     @property
     def dim_1(self):
         if self._dim_1 is None and self.master_file and os.path.exists(self.master_file):
-            with h5py.File(self.master_file, 'r') as h5_file:
-                assert self._DET_META_PATH in h5_file[self._entry]
-                self._dim_1 = h5_file[self._entry][self._DET_META_PATH]['size'][0]
+            if self.projections is not None:
+                if len(self.projections) > 0:
+                    self._dim_1, self._dim_2 = get_data(self.projections[0]).shape
         return self._dim_1
 
     @property
     def dim_2(self):
         if self._dim_2 is None and self.master_file and os.path.exists(self.master_file):
-            with h5py.File(self.master_file, 'r') as h5_file:
-                assert self._DET_META_PATH in h5_file[self._entry]
-                self._dim_2 = h5_file[self._entry][self._DET_META_PATH]['size'][()][1]
+            if self.projections is not None:
+                if len(self.projections) > 0:
+                    self._dim_1, self._dim_2 = get_data(self.projections[0]).shape
         return self._dim_2
 
     @property
@@ -458,14 +457,17 @@ class HDF5TomoScan(TomoScanBase):
 
     @docstring(TomoScanBase.get_proj_angle_url)
     def get_proj_angle_url(self) -> dict:
-        res = {}
-        if self.projections is not None:
-            for frame in self.projections:
-                res[frame.rotation_angle] = frame.url
-        if self.return_projs:
-            for frame in self.return_projs:
-                res[str(frame.rotation_angle) + '(1)'] = frame.url
-        return res
+        if self.frames is not None:
+            res = {}
+            for frame in self.frames:
+                if frame.image_key is ImageKey.PROJECTION:
+                    if frame.is_return is False:
+                        res[frame.rotation_angle] = frame.url
+                    else:
+                        res[str(frame.rotation_angle) + '(1)'] = frame.url
+            return res
+        else:
+            return None
 
     def __str__(self):
         return 'hdf5 scan(path: %s, master_file: %s, entry: %s)' % (self.path,

tomoscan/esrf/test/test_hdf5scan.py

@@ -163,34 +163,31 @@ class TestHDF5Scan(HDF5TestBaseClass):
 
     def testFlats(self):
         """Make sure flats are valid"""
+        n_flats = 42
+        flats = self.scan.flats
+        self.assertEqual(len(flats), n_flats)
+        self.assertEqual(self.scan.ref_n, n_flats)
         with self.assertRaises(NotImplementedError):
-            flats = self.scan.flats
-        n_ref = 21
-        self.assertEqual(self.scan.ref_n, n_ref)
+            self.scan.ff_interval
 
-        # for now not implemented
-        # not implemented at the moment
-        data = numpy.arange(2048*2048)
-        data.reshape(2048, 2048)
-        # not implemented at the moment
-        self.assertEqual(self.scan.ff_interval, 21)
+    def testDims(self):
+        self.assertEqual(self.scan.dim_1, 20)
+        self.assertEqual(self.scan.dim_2, 20)
 
     def testAxisUtils(self):
-        self.assertEqual(self.scan.scan_range, 360)
-        self.assertEqual(self.scan.tomo_n, 100)
-        # self.assertEqual(self.scan.dim_1, 2048)
-        # self.assertEqual(self.scan.dim_2, 2048)
+        self.assertEqual(self.scan.scan_range, 180)
+        self.assertEqual(self.scan.tomo_n, 1500)
 
-        proj0_file_path = '../../../../../../users/opid19/W:/clemence/visualtomo/data_test2/tomo0001/tomo_0000.h5'
         radios_urls_evolution = self.scan.get_proj_angle_url()
-        self.assertEquals(len(radios_urls_evolution), 100)
-        self.assertEquals(radios_urls_evolution[0].file_path(), proj0_file_path)
-        self.assertEquals(radios_urls_evolution[0].data_slice(), ('0',))
-        self.assertEquals(radios_urls_evolution[0].data_path(), '/entry_0000/measurement/pcoedge64/data')
+        self.assertEquals(len(radios_urls_evolution), 1503)
+        self.assertEquals(radios_urls_evolution[0].file_path(), self.scan.master_file)
+        self.assertEquals(radios_urls_evolution[0].data_slice(), 22)
+        self.assertEquals(radios_urls_evolution[0].data_path(), '/entry0000/instrument/detector/data')
 
     def testDarkRefUtils(self):
-        self.assertEqual(self.scan.tomo_n, 100)
-        self.assertEqual(self.scan.pixel_size[1], 6.5)
+        self.assertEqual(self.scan.tomo_n, 1500)
+        # TODO: add after merge
+        # self.assertTrue(numpy.isclose(self.scan.get_pixel_size(unit='mm'), 0.05))
 
 
 def suite():