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

tomoscan/esrf/edfscan.py

@@ -85,8 +85,10 @@ class EDFTomoScan(TomoScanBase):
         self.__scan_range = None
         self._edf_n_frames = n_frames
         self.__distance = None
+        self.__energy = None
         self.update()
 
+
     @docstring(TomoScanBase.clear_caches)
     def clear_caches(self):
         self._darks = None
@@ -422,7 +424,7 @@ class EDFTomoScan(TomoScanBase):
         if self.__distance is None:
             return None
         else:
-            return self.__distance
+            return self.__distance * MetricSystem.MILLIMETER.value
 
     @property
     @docstring(TomoScanBase.energy)
@@ -457,7 +459,7 @@ class EDFTomoScan(TomoScanBase):
         # for now pixel size are stored in microns.
         # We want to return them in meter
         if value is not None:
-            return value * MetricSystem.MICROMETER
+            return value * MetricSystem.MICROMETER.value
         else:
             return None
 

tomoscan/esrf/hdf5scan.py

@@ -90,6 +90,8 @@ class HDF5TomoScan(TomoScanBase):
 
     _DISTANCE_PATH = 'instrument/detector/distance'
 
+    _ENERGY_PATH = 'beam/incident_energy'
+
     _SCHEME = 'silx'
 
     _EPSILON_ROT_ANGLE = 0.02
@@ -148,6 +150,7 @@ class HDF5TomoScan(TomoScanBase):
         self._image_keys = None
         self._rotation_angles = None
         self._distance = None
+        self._energy = None
 
     @staticmethod
     def get_master_file(scan_path):
@@ -483,6 +486,15 @@ class HDF5TomoScan(TomoScanBase):
                 self._distance = self._get_value(distance_dataset, default_unit='m')
         return self._distance
 
+    @property
+    def energy(self) -> typing.Union[None, float]:
+        if (self._energy is None and self.master_file and
+                os.path.exists(self.master_file)):
+            with h5py.File(self.master_file, 'r') as h5_file:
+                energy_dataset = h5_file[self._entry][self._ENERGY_PATH]
+                self._energy = self._get_value(energy_dataset, default_unit='keV')
+        return self._energy
+
     @property
     def frames(self) -> typing.Union[None, tuple]:
         """return tuple of frames. Frames contains """

tomoscan/unitsystem/metricsystem.py

@@ -29,9 +29,50 @@ __date__ = "01/09/2016"
 
 from silx.utils.enum import Enum as _Enum
 
+# Constants
+_elementary_charge_coulomb = 1.602176634e-19
 
-_meter = 1.0
 
+_joule_si = 1.0
+class EnergySI(_Enum):
+    """Util enum for energy in SI units (Joules)"""
+    JOULE = _joule_si
+    ELEMCHARGE = _elementary_charge_coulomb
+    ELECTRONVOLT = _elementary_charge_coulomb
+
+    KILOELECTRONVOLT = _elementary_charge_coulomb * 1e3
+    KILOJOULE = 1e3 * _joule_si
+
+    @classmethod
+    def from_value(cls, value):
+        if isinstance(value, str):
+            return cls.from_str(value=value)
+        else:
+            _Enum.from_value(value=value)
+
+    @classmethod
+    def from_str(cls, value: str):
+        assert isinstance(value, str)
+        if value.lower() in ('e', 'qe'):
+            return EnergySI.ELEMCHARGE
+        elif value.lower() in ("j", "joule"):
+            return EnergySI.JOULE
+        elif value.lower() in ("kj", "kilojoule"):
+            return EnergySI.KILOJOULE
+        elif value.lower() in ("ev", "electronvolt"):
+            return EnergySI.ELECTRONVOLT
+        elif value.lower() in ("kev", "kiloelectronvolt"):
+            return EnergySI.KILOELECTRONVOLT
+        else:
+            raise ValueError("Cannot convert: %s" % value)
+
+
+# Default units:
+#  - lenght: meter (m)
+#  - energy: kilo Electronvolt (keV)
+_meter = 1.0
+_kev = 1.0
+_joule_kev = 1./EnergySI.KILOELECTRONVOLT.value
 
 class MetricSystem(_Enum):
     """Util enum to retrieve metric"""
@@ -42,6 +83,12 @@ class MetricSystem(_Enum):
     MICROMETER = _meter * 1e-6
     NANOMETER = _meter * 1e-9
 
+    KILOELECTRONVOLT = _kev
+    ELECTRONVOLT = _kev * 1e-3
+    JOULE = _kev / EnergySI.KILOELECTRONVOLT.value
+    KILOJOULE = _kev / EnergySI.KILOELECTRONVOLT.value * 1e3
+
+
     @classmethod
     def from_value(cls, value):
         if isinstance(value, str):
@@ -62,6 +109,14 @@ class MetricSystem(_Enum):
             return MetricSystem.MICROMETER
         elif value.lower() in ('nm', 'nanometer'):
             return MetricSystem.NANOMETER
+        elif value.lower() in ('kev', 'kiloelectronvolt'):
+            return MetricSystem.KILOELECTRONVOLT
+        elif value.lower() in ('ev', 'electronvolt'):
+            return MetricSystem.ELECTRONVOLT
+        elif value.lower() in ('j', 'joule'):
+            return MetricSystem.JOULE
+        elif value.lower() in ('kj', 'kilojoule'):
+            return MetricSystem.KILOJOULE
         else:
             raise ValueError("Cannot convert: %s" % value)