Merge branch 'change_extra_params_names' into 'master'

h52nx: rename keys for extra parameters when provided by the configuration file

See merge request !78

nxtomomill/converter/hdf5/acquisition/standardacquisition.py

@@ -538,18 +538,35 @@ class StandardAcquisition(BaseAcquisition):
         )
         return values, unit
 
+    def get_already_defined_params(self, key):
+        defined = self.__get_extra_param(key=key)
+        if len(defined) > 1:
+            raise ValueError("{} are aliases. Only one should be defined")
+        elif len(defined) == 0:
+            return None
+        else:
+            return list(defined.values())[0]
+
+    def __get_extra_param(self, key) -> dict:
+        """return already defined parameters for one key.
+        A key as aliases so it returns a dict"""
+        aliases = list(TomoHDF5Config.EXTRA_PARAMS_ALIASES[key])
+        aliases.append(key)
+        res = {}
+        for alias in aliases:
+            if alias in self.configuration.param_already_defined:
+                res[alias] = self.configuration.param_already_defined[alias]
+        return res
+
     def _write_beam(self, root_node, request_input, input_callback):
         instrument_node = root_node.require_group("instrument")
         beam_node = instrument_node.require_group("beam")
-        if (
-            TomoHDF5Config.EXTRA_PARAMS_ENERGY_DK
-            in self.configuration.param_already_defined
-        ):
-            energy = float(
-                self.configuration.param_already_defined[
-                    TomoHDF5Config.EXTRA_PARAMS_ENERGY_DK
-                ]
-            )
+
+        already_defined = self.get_already_defined_params(
+            key=TomoHDF5Config.EXTRA_PARAMS_ENERGY_DK
+        )
+        if already_defined is not None:
+            energy = float(already_defined)
             unit = "kev"
         else:
             energy, unit = self._get_energy(
@@ -583,15 +600,11 @@ class StandardAcquisition(BaseAcquisition):
             detector_node["count_time"] = self._acq_expo_time
             detector_node["count_time"].attrs["unit"] = "s"
         # write distance
-        if (
-            TomoHDF5Config.EXTRA_PARAMS_DISTANCE
-            in self.configuration.param_already_defined
-        ):
-            distance = float(
-                self.configuration.param_already_defined[
-                    TomoHDF5Config.EXTRA_PARAMS_DISTANCE
-                ]
-            )
+        already_defined = self.get_already_defined_params(
+            key=TomoHDF5Config.EXTRA_PARAMS_DISTANCE
+        )
+        if already_defined is not None:
+            distance = float(already_defined)
             unit = "m"
         else:
             distance, unit = self._get_distance()
@@ -601,15 +614,11 @@ class StandardAcquisition(BaseAcquisition):
         # write x and y pixel size
         # if magnified pixel size is found then we right this value.
         # otherwise will take pixel size (if found)
-        if (
-            TomoHDF5Config.EXTRA_PARAMS_X_PIXEL_SIZE_DK
-            in self.configuration.param_already_defined
-        ):
-            x_pixel_size = float(
-                self.configuration.param_already_defined[
-                    TomoHDF5Config.EXTRA_PARAMS_X_PIXEL_SIZE_DK
-                ]
-            )
+        already_defined = self.get_already_defined_params(
+            key=TomoHDF5Config.EXTRA_PARAMS_X_PIXEL_SIZE_DK
+        )
+        if already_defined is not None:
+            x_pixel_size = float(already_defined)
             unit = "m"
         else:
             x_pixel_size, unit = self._get_pixel_size("x")
@@ -617,15 +626,11 @@ class StandardAcquisition(BaseAcquisition):
             detector_node["x_pixel_size"] = x_pixel_size
             detector_node["x_pixel_size"].attrs["unit"] = unit
 
-        if (
-            TomoHDF5Config.EXTRA_PARAMS_Y_PIXEL_SIZE_DK
-            in self.configuration.param_already_defined
-        ):
-            y_pixel_size = float(
-                self.configuration.param_already_defined[
-                    TomoHDF5Config.EXTRA_PARAMS_Y_PIXEL_SIZE_DK
-                ]
-            )
+        already_defined = self.get_already_defined_params(
+            key=TomoHDF5Config.EXTRA_PARAMS_Y_PIXEL_SIZE_DK
+        )
+        if already_defined is not None:
+            y_pixel_size = float(already_defined)
             unit = "m"
         else:
             y_pixel_size, unit = self._get_pixel_size("y")

nxtomomill/io/config.py

@@ -254,18 +254,33 @@ class TomoHDF5Config:
 
     EXTRA_PARAMS_SECTION_DK = "EXTRA_PARAMS_SECTION"
 
-    EXTRA_PARAMS_ENERGY_DK = "energy"
-    EXTRA_PARAMS_X_PIXEL_SIZE_DK = "x_pixel_size"
-    EXTRA_PARAMS_Y_PIXEL_SIZE_DK = "y_pixel_size"
-    EXTRA_PARAMS_DISTANCE = "detector_sample_distance"
+    EXTRA_PARAMS_ENERGY_DK = "energy_kev"
+    EXTRA_PARAMS_ENERGY_DK_ALIASES = ("energy",)
+    EXTRA_PARAMS_X_PIXEL_SIZE_DK = "x_pixel_size_m"
+    EXTRA_PARAMS_X_PIXEL_SIZE_DK_ALIASES = ("x_pixel_size",)
+    EXTRA_PARAMS_Y_PIXEL_SIZE_DK = "y_pixel_size_m"
+    EXTRA_PARAMS_Y_PIXEL_SIZE_DK_ALIASES = ("y_pixel_size",)
+    EXTRA_PARAMS_DISTANCE = "detector_sample_distance_m"
+    EXTRA_PARAMS_DISTANCE_ALIASES = ("detector_sample_distance",)
 
     EXTRA_PARAMS_ENERGY_VALID_KEYS = (
         EXTRA_PARAMS_ENERGY_DK,
+        *EXTRA_PARAMS_ENERGY_DK_ALIASES,
         EXTRA_PARAMS_X_PIXEL_SIZE_DK,
+        *EXTRA_PARAMS_X_PIXEL_SIZE_DK_ALIASES,
         EXTRA_PARAMS_Y_PIXEL_SIZE_DK,
+        *EXTRA_PARAMS_Y_PIXEL_SIZE_DK_ALIASES,
         EXTRA_PARAMS_DISTANCE,
+        *EXTRA_PARAMS_DISTANCE_ALIASES,
     )
 
+    EXTRA_PARAMS_ALIASES = {
+        EXTRA_PARAMS_ENERGY_DK: EXTRA_PARAMS_ENERGY_DK_ALIASES,
+        EXTRA_PARAMS_X_PIXEL_SIZE_DK: EXTRA_PARAMS_X_PIXEL_SIZE_DK_ALIASES,
+        EXTRA_PARAMS_Y_PIXEL_SIZE_DK: EXTRA_PARAMS_Y_PIXEL_SIZE_DK_ALIASES,
+        EXTRA_PARAMS_DISTANCE: EXTRA_PARAMS_DISTANCE_ALIASES,
+    }
+
     COMMENTS_EXTRA_PARAMS_SECTION = {
         EXTRA_PARAMS_SECTION_DK: "optional section\n"
         "# you can predefined values which are missing in the input .h5 file\n"

nxtomomill/io/confighandler.py

@@ -50,12 +50,14 @@ SETTABLE_PARAMETERS_UNITS = {
     "energy": "kev",
     "x_pixel_size": "m",
     "y_pixel_size": "m",
+    "detector_sample_distance": "m",
 }
 
 SETTABLE_PARAMETERS_TYPE = {
     "energy": float,
     "x_pixel_size": float,
     "y_pixel_size": float,
+    "detector_sample_distance": float,
 }
 
 SETTABLE_PARAMETERS = SETTABLE_PARAMETERS_UNITS.keys()