[HDF5Tomoscan] add {x/y/z}translation properties

tomoscan/esrf/hdf5scan.py

@@ -89,6 +89,12 @@ class HDF5TomoScan(TomoScanBase):
 
     _ROTATION_ANGLE_PATH = "sample/rotation_angle"
 
+    _X_TRANS_PATH = "sample/x_translation"
+
+    _Y_TRANS_PATH = "sample/y_translation"
+
+    _Z_TRANS_PATH = "sample/z_translation"
+
     _IMG_KEY_PATH = "instrument/detector/image_key"
 
     _IMG_KEY_CONTROL_PATH = "instrument/detector/image_key_control"
@@ -184,6 +190,9 @@ class HDF5TomoScan(TomoScanBase):
         self._estimated_cor_frm_motor = None
         self._start_time = None
         self._end_time = None
+        self._x_translations = None
+        self._y_translations = None
+        self._z_translations = None
 
     @staticmethod
     def get_master_file(scan_path):
@@ -221,6 +230,9 @@ class HDF5TomoScan(TomoScanBase):
         self._distance = None
         self._fov = None
         self._image_keys_control = None
+        self._x_translations = None
+        self._y_translations = None
+        self._z_translations = None
 
     @staticmethod
     def _get_entry_at(index: int, file_path: str) -> str:
@@ -465,7 +477,7 @@ class HDF5TomoScan(TomoScanBase):
             return None
 
     @property
-    def rotation_angle(self) -> typing.Union[None, list]:
+    def rotation_angle(self) -> typing.Union[None, tuple]:
         if self._rotation_angles is None:
             self._check_hdf5scan_validity()
             with HDF5File(self.master_file, "r", swmr=True) as h5_file:
@@ -478,6 +490,42 @@ class HDF5TomoScan(TomoScanBase):
                 )
         return self._rotation_angles
 
+    @property
+    def x_translation(self) -> typing.Union[None, tuple]:
+        if self._x_translations is None:
+            self._check_hdf5scan_validity()
+            with HDF5File(self.master_file, "r", swmr=True) as h5_file:
+                _translations = h5_file[self._entry][self._X_TRANS_PATH][()]
+                # cast in float
+                self._x_translations = tuple(
+                    [float(trans) for trans in _translations]
+                )
+        return self._x_translations
+
+    @property
+    def y_translation(self) -> typing.Union[None, tuple]:
+        if self._y_translations is None:
+            self._check_hdf5scan_validity()
+            with HDF5File(self.master_file, "r", swmr=True) as h5_file:
+                _translations = h5_file[self._entry][self._Y_TRANS_PATH][()]
+                # cast in float
+                self._y_translations = tuple(
+                    [float(trans) for trans in _translations]
+                )
+        return self._y_translations
+
+    @property
+    def z_translation(self) -> typing.Union[None, tuple]:
+        if self._z_translations is None:
+            self._check_hdf5scan_validity()
+            with HDF5File(self.master_file, "r", swmr=True) as h5_file:
+                _translations = h5_file[self._entry][self._Z_TRANS_PATH][()]
+                # cast in float
+                self._z_translations = tuple(
+                    [float(trans) for trans in _translations]
+                )
+        return self._z_translations
+
     @property
     def image_key(self) -> typing.Union[list, None]:
         if self._entry and self._image_keys is None:
@@ -729,6 +777,9 @@ class HDF5TomoScan(TomoScanBase):
         if self._frames is None:
             image_keys = self.image_key
             rotation_angles = self.rotation_angle
+            x_translation = self.x_translation
+            y_translation = self.y_translation
+            z_translation = self.z_translation
             if len(image_keys) != len(rotation_angles):
                 raise ValueError(
                     "`rotation_angle` and `image_key` have "
@@ -759,8 +810,9 @@ class HDF5TomoScan(TomoScanBase):
             delta_angle = None
             last_proj_frame = None
             return_already_reach = False
-            for i_frame, rot_a, img_key in zip(
-                range(len(rotation_angles)), rotation_angles, image_keys
+            for i_frame, rot_a, img_key, x_tr, y_tr, z_tr in zip(
+                range(len(rotation_angles)), rotation_angles, image_keys,
+                x_translation, y_translation, z_translation
             ):
                 url = DataUrl(
                     file_path=self.master_file,
@@ -770,7 +822,13 @@ class HDF5TomoScan(TomoScanBase):
                 )
 
                 frame = Frame(
-                    index=i_frame, url=url, image_key=img_key, rotation_angle=rot_a
+                    index=i_frame,
+                    url=url,
+                    image_key=img_key,
+                    rotation_angle=rot_a,
+                    x_translation=x_tr,
+                    y_translation=y_tr,
+                    z_translation=z_tr,
                 )
                 if self.image_key_control is not None:
                     is_control_frame = (
@@ -862,6 +920,9 @@ class Frame:
         image_key: typing.Union[None, ImageKey, int] = None,
         rotation_angle: typing.Union[None, float] = None,
         is_control_proj: bool = False,
+        x_translation: typing.Union[None, float]=None,
+        y_translation: typing.Union[None, float] = None,
+        z_translation: typing.Union[None, float] = None,
     ):
         assert type(index) is int
         self._index = index
@@ -870,6 +931,9 @@ class Frame:
         self._url = url
         self._is_control_frame = is_control_proj
         self._data = None
+        self._x_translation = x_translation
+        self._y_translation = y_translation
+        self._z_translation = z_translation
 
     @property
     def index(self) -> int:
@@ -899,6 +963,18 @@ class Frame:
     def is_control(self) -> bool:
         return self._is_control_frame
 
+    @property
+    def x_translation(self):
+        return self._x_translation
+
+    @property
+    def y_translation(self):
+        return self._y_translation
+
+    @property
+    def z_translation(self):
+        return self._z_translation
+
     @is_control.setter
     def is_control(self, is_return: bool):
         self._is_control_frame = is_return
@@ -908,11 +984,17 @@ class Frame:
             "Frame {index},: image_key: {image_key},"
             "is_control: {is_control},"
             "rotation_angle: {rotation_angle},"
+            "x_translation: {x_translation},"
+            "y_translation: {y_translation},"
+            "z_translation: {z_translation},"
             "url: {url}".format(
                 index=self.index,
                 image_key=self.image_key,
                 is_control=self.is_control,
                 rotation_angle=self.rotation_angle,
                 url=self.url.path(),
+                x_translation=self.x_translation,
+                y_translation=self.y_translation,
+                z_translation=self.z_translation,
             )
         )