Merge branch 'add_hdf5' of gitlab.esrf.fr:tomotools/tomoscan into add_hdf5

tomoscan/esrf/hdf5scan.py

@@ -293,34 +293,40 @@ class HDF5TomoScan(TomoScanBase):
 
     @property
     @docstring(TomoScanBase.projections)
-    def projections(self) -> typing.Union[list, None]:
+    def projections(self) -> typing.Union[dict, None]:
         """projections / radio, does not include the return projections"""
         if self._projections is None:
             if self.frames:
                 proj_frames = tuple(filter(lambda x: x.image_key is ImageKey.PROJECTION and x.is_return is False, self.frames))
-                self._projections = [proj_frame.url for proj_frame in proj_frames]
+                self._projections = {}
+                for proj_frame in proj_frames:
+                    self._projections[proj_frame.index] = proj_frame.url
         return self._projections
 
     @projections.setter
-    def projections(self, projections: list):
+    def projections(self, projections: dict):
         self._projections = projections
 
     @property
     @docstring(TomoScanBase.darks)
-    def darks(self) -> typing.Union[list, None]:
+    def darks(self) -> typing.Union[dict, None]:
         if self._darks is None:
             if self.frames:
                 dark_frames = tuple(filter(lambda x: x.image_key is ImageKey.DARK_FIELD, self.frames))
-                self._darks = [dark_frame.url for dark_frame in dark_frames]
+                self._darks = {}
+                for dark_frame in dark_frames:
+                    self._darks[dark_frame.index] = dark_frame.url
         return self._darks
 
     @property
     @docstring(TomoScanBase.flats)
-    def flats(self) -> typing.Union[list, None]:
+    def flats(self) -> typing.Union[dict, None]:
         if self._flats is None:
             if self.frames:
                 flat_frames = tuple(filter(lambda x: x.image_key is ImageKey.FLAT_FIELD, self.frames))
-                self._flats = [flat_frame.url for flat_frame in flat_frames]
+                self._flats = {}
+                for flat_frame in flat_frames:
+                    self._flats[flat_frame.index] = flat_frame.url
         return self._flats
 
     @docstring(TomoScanBase.update)
@@ -432,7 +438,7 @@ class HDF5TomoScan(TomoScanBase):
         if self._dim_1 is None and self.master_file and os.path.exists(self.master_file):
             if self.projections is not None:
                 if len(self.projections) > 0:
-                    self._dim_1, self._dim_2 = get_data(self.projections[0]).shape
+                    self._dim_1, self._dim_2 = get_data(list(self.projections.values())[0]).shape
         return self._dim_1
 
     @property
@@ -440,7 +446,7 @@ class HDF5TomoScan(TomoScanBase):
         if self._dim_2 is None and self.master_file and os.path.exists(self.master_file):
             if self.projections is not None:
                 if len(self.projections) > 0:
-                    self._dim_1, self._dim_2 = get_data(self.projections[0]).shape
+                    self._dim_1, self._dim_2 = get_data(list(self.projections.values())[0]).shape
         return self._dim_2
 
     @property

tomoscan/esrf/test/test_edfscan.py

@@ -259,7 +259,9 @@ class TestProjections(unittest.TestCase):
         self.assertEqual(len(scan.projections), 3)
         scan.update()
         self.assertEqual(len(scan.projections), 4)
-        self.assertTrue(isinstance(scan.projections[0], silx.io.url.DataUrl))
+
+        index_0 = list(scan.projections.keys())[0]
+        self.assertTrue(isinstance(scan.projections[index_0], silx.io.url.DataUrl))
 
     def testProjectionWithExtraRadio(self):
         mock = MockEDF(scan_path=self.folder, n_radio=11, n_extra_radio=2,

tomoscan/esrf/test/test_hdf5scan.py

@@ -150,7 +150,7 @@ class TestHDF5Scan(HDF5TestBaseClass):
         """Make sure projections are valid"""
         projections = self.scan.projections
         self.assertEqual(len(self.scan.projections), 1500)
-        url_0 = projections[0]
+        url_0 = projections[list(projections.keys())[0]]
         self.assertEqual(url_0.file_path(), os.path.join(self.scan.master_file))
         self.assertEqual(url_0.data_slice(), 22)
 

tomoscan/scanbase.py

@@ -117,7 +117,7 @@ class TomoScanBase:
         self._flats = flats
 
     @property
-    def darks(self) -> Union[None,dict]:
+    def darks(self) -> Union[None, dict]:
         """list of darks files"""
         return self._darks