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

tomoscan/esrf/hdf5scan.py

@@ -46,8 +46,9 @@ _logger = logging.getLogger(__name__)
 
 
 class ImageKey(_Enum):
-    PROJECTION = 0,
-    FLAT_FIELD = 1,
+    ALIGNMENT = -1
+    PROJECTION = 0
+    FLAT_FIELD = 1
     DARK_FIELD = 2
     INVALID = 3
 
@@ -303,7 +304,7 @@ class HDF5TomoScan(TomoScanBase):
         """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_control is False, self.frames))
+                proj_frames = tuple(filter(lambda x: x.image_key == ImageKey.PROJECTION and x.is_control == False, self.frames))
                 self._projections = {}
                 for proj_frame in proj_frames:
                     self._projections[proj_frame.index] = proj_frame.url
@@ -318,7 +319,7 @@ class HDF5TomoScan(TomoScanBase):
     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))
+                dark_frames = tuple(filter(lambda x: x.image_key == ImageKey.DARK_FIELD, self.frames))
                 self._darks = {}
                 for dark_frame in dark_frames:
                     self._darks[dark_frame.index] = dark_frame.url
@@ -329,7 +330,7 @@ class HDF5TomoScan(TomoScanBase):
     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))
+                flat_frames = tuple(filter(lambda x: x.image_key == ImageKey.FLAT_FIELD, self.frames))
                 self._flats = {}
                 for flat_frame in flat_frames:
                     self._flats[flat_frame.index] = flat_frame.url
@@ -379,7 +380,7 @@ class HDF5TomoScan(TomoScanBase):
         """"""
         frames = self.frames
         if frames:
-            return_frames = list(filter(lambda x: x.is_control is True, frames))
+            return_frames = list(filter(lambda x: x.is_control == True, frames))
             return return_frames
         else:
             return None
@@ -453,18 +454,14 @@ class HDF5TomoScan(TomoScanBase):
 
     @property
     def dim_1(self) -> typing.Union[None, int]:
-        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(list(self.projections.values())[0]).shape
+        if self._dim_1 is None:
+            self._get_dim1_dim2()
         return self._dim_1
 
     @property
     def dim_2(self) -> typing.Union[None, int]:
-        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(list(self.projections.values())[0]).shape
+        if self._dim_2 is None:
+            self._get_dim1_dim2()
         return self._dim_2
 
     @property
@@ -483,11 +480,17 @@ class HDF5TomoScan(TomoScanBase):
         """read x and y pixel values"""
         with h5py.File(self.master_file, 'r') as h5_file:
             x_pixel_dataset = h5_file[self._entry][self._X_PIXEL_SIZE_PATH]
-            _x_pixel_size = self._get_value(x_pixel_dataset, default_unit='mm')
+            _x_pixel_size = self._get_value(x_pixel_dataset, default_unit='micrometer')
             y_pixel_dataset = h5_file[self._entry][self._Y_PIXEL_SIZE_PATH]
-            _y_pixel_size = self._get_value(y_pixel_dataset, default_unit='mm')
+            _y_pixel_size = self._get_value(y_pixel_dataset, default_unit='micrometer')
         return _x_pixel_size, _y_pixel_size
 
+    def _get_dim1_dim2(self):
+        if self.master_file and os.path.exists(self.master_file):
+            if self.projections is not None:
+                if len(self.projections) > 0:
+                    self._dim_2, self._dim_1 = get_data(list(self.projections.values())[0]).shape
+
     @property
     def y_pixel_size(self) -> typing.Union[None, float]:
         if (self._y_pixel_size is None and self.master_file and
@@ -553,14 +556,14 @@ class HDF5TomoScan(TomoScanBase):
                 frame = Frame(index=i_frame, url=url, image_key=img_key,
                               rotation_angle=rot_a)
                 if self.image_key_control is not None:
-                    is_control_frame = self.image_key_control[frame.index]
+                    is_control_frame = (self.image_key_control[frame.index] == ImageKey.ALIGNMENT.value)
                 else:
                     return_already_reach, delta_angle = is_return(lframe=frame,
                                                                   llast_proj_frame=last_proj_frame,
                                                                   ldelta_angle=delta_angle,
                                                                   return_already_reach=return_already_reach)
                     is_control_frame = return_already_reach
-                frame.is_control_frame = is_control_frame
+                frame._is_control_frame = is_control_frame
                 self._frames.append(frame)
                 last_proj_frame = frame
             self._frames = tuple(self._frames)