Merge branch 'add_alignment_proj_property' into 'master'

add alignment_projections property

See merge request !26

doc/tutorials/edf_scan.ipynb

@@ -166,7 +166,7 @@
    ],
    "source": [
     "from silx.io.utils import get_data\n",
-    "frame_28_data = get_data(scan.projections[28])\n",
+    "frame_18_data = get_data(scan.projections[18])\n",
     "# imshow(frame_28_data)"
    ]
   },

tomoscan/esrf/edfscan.py

@@ -77,7 +77,6 @@ class EDFTomoScan(TomoScanBase):
         # data caches
         self._darks = None
         self._flats = None
-        self._projections = None
         self.__tomo_n = None
         self.__ref_n = None
         self.__dark_n = None
@@ -243,9 +242,27 @@ class EDFTomoScan(TomoScanBase):
     @docstring(TomoScanBase.update)
     def update(self):
         if self.path is not None:
-            self.projections = EDFTomoScan.get_proj_urls(
+            all_projections = EDFTomoScan.get_proj_urls(
                 self.path, n_frames=self._edf_n_frames
             )
+
+            def select_proj(ddict, from_, to_):
+                indexes = sorted(set(ddict.keys()))
+                sel_indexes = indexes[from_:to_]
+                res = {}
+                for index in sel_indexes:
+                    res[index] = ddict[index]
+                return res
+
+            if self.tomo_n is not None and len(all_projections) > self.tomo_n:
+                self._projections = select_proj(all_projections, 0, self.tomo_n)
+                self._alignment_projections = select_proj(
+                    all_projections, self.tomo_n, None
+                )
+            else:
+                self._projections = all_projections
+                self._alignment_projections = {}
+
             self._darks = EDFTomoScan.get_darks_url(self.path)
             self._flats = EDFTomoScan.get_refs_url(self.path)
 

tomoscan/esrf/hdf5scan.py

@@ -145,7 +145,6 @@ class HDF5TomoScan(TomoScanBase):
         # for now the default entry is 1_tomo but should change with time
 
         # data caches
-        self._projections = None
         self._projections_compacted = None
         self._flats = None
         self._darks = None
@@ -327,7 +326,6 @@ class HDF5TomoScan(TomoScanBase):
     @property
     @docstring(TomoScanBase.projections)
     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(
@@ -346,6 +344,23 @@ class HDF5TomoScan(TomoScanBase):
     def projections(self, projections: dict):
         self._projections = projections
 
+    @property
+    @docstring(TomoScanBase.alignment_projections)
+    def alignment_projections(self) -> typing.Union[dict, None]:
+        if self._alignment_projections is None:
+            if self.frames:
+                proj_frames = tuple(
+                    filter(
+                        lambda x: x.image_key == ImageKey.PROJECTION
+                        and x.is_control == True,
+                        self.frames,
+                    )
+                )
+                self._alignment_projections = {}
+                for proj_frame in proj_frames:
+                    self._alignment_projections[proj_frame.index] = proj_frame.url
+        return self._alignment_projections
+
     @property
     @docstring(TomoScanBase.darks)
     def darks(self) -> typing.Union[dict, None]:
@@ -833,3 +848,17 @@ class Frame:
     @is_control.setter
     def is_control(self, is_return: bool):
         self._is_control_frame = is_return
+
+    def __str__(self):
+        return (
+            "Frame {index},: image_key: {image_key},"
+            "is_control: {is_control},"
+            "rotation_angle: {rotation_angle},"
+            "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(),
+            )
+        )

tomoscan/esrf/test/test_edfscan.py

@@ -302,7 +302,8 @@ class TestProjections(unittest.TestCase):
         )
         mock.end_acquisition()
         scan = EDFTomoScan(scan=self.folder)
-        self.assertEqual(len(scan.projections), 11 + 2)
+        self.assertEqual(len(scan.projections), 11)
+        self.assertEqual(len(scan.alignment_projections), 2)
         proj_angle_dict = scan.get_proj_angle_url()
         self.assertEqual(len(proj_angle_dict), 11 + 2)
         self.assertTrue(90 in proj_angle_dict)

tomoscan/esrf/test/test_hdf5scan.py

@@ -153,6 +153,10 @@ class TestHDF5Scan(HDF5TestBaseClass):
         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)
+        # should be 4 but angles are truely missleading: 179.88, 180.0, 90, 0.
+        # in this case we are not using any information from image_key_control
+        # and we wait deduce 'return mode' from angles.
+        self.assertEqual(len(self.scan.alignment_projections), 3)
 
     def testDark(self):
         """Make sure darks are valid"""

tomoscan/scanbase.py

@@ -174,13 +174,26 @@ class TomoScanBase:
 
     @property
     def projections(self) -> Union[None, dict]:
-        """list of projections files"""
+        """if found dict of projections urls with index during acquisition as
+        key"""
         return self._projections
 
     @projections.setter
     def projections(self, projections: dict) -> None:
         self._projections = projections
 
+    @property
+    def alignment_projections(self) -> Union[None, dict]:
+        """
+        dict of projections made for alignment with acquisition index as key
+        None if not found
+        """
+        return self._alignment_projections
+
+    @alignment_projections.setter
+    def alignment_projections(self, alignment_projs):
+        self._alignment_projections = alignment_projs
+
     @property
     def dark_n(self) -> Union[None, int]:
         raise NotImplementedError("Base class")