one more step on addinf 3D-XRD. Add rocking and base tilt datasets

nxtomomill/app/h5_3dxrd2nx.py

@@ -40,6 +40,7 @@ from nxtomomill.io.confighandler import XRD3DHDF5ConfigHandler
 from nxtomomill.io.confighandler import SETTABLE_PARAMETERS_UNITS
 from collections.abc import Iterable
 from nxtomomill.utils import Format
+from nxtomomill.io.config import XRD3DHDF5Config
 import argparse
 
 
@@ -92,13 +93,13 @@ def main(argv):
         "--file_extension",
         default=None,
         help="extension of the output file. Valid values are "
-             "" + "/".join(utils.FileExtension.values()),
+        "" + "/".join(utils.FileExtension.values()),
     )
     parser.add_argument(
         "--single-file",
         help="merge all scan sequence to the same output file. "
-             "By default create one file per sequence and "
-             "group all sequence in the output file",
+        "By default create one file per sequence and "
+        "group all sequence in the output file",
         dest="single_file",
         action="store_true",
         default=None,
@@ -118,7 +119,7 @@ def main(argv):
     parser.add_argument(
         "--entries",
         help="Specify (root) entries to be converted. By default it will try "
-             "to convert all existing entries.",
+        "to convert all existing entries.",
         default=None,
     )
     parser.add_argument(
@@ -129,14 +130,14 @@ def main(argv):
     parser.add_argument(
         "--raises-error",
         help="Raise errors if some data are not met instead of providing some"
-             " default values",
+        " default values",
         action="store_true",
         default=None,
     )
     parser.add_argument(
         "--field-of-view",
         help="Force the output to be `Half`  or `Full` acquisition. Otherwise "
-             "parse raw data to find this information.",
+        "parse raw data to find this information.",
         default=None,
     )
     parser.add_argument(
@@ -185,8 +186,8 @@ def main(argv):
         "--valid-camera-names",
         default=None,
         help="Valid NXDetector dataset name to be considered. Otherwise will"
-             "try to deduce them from NX_class attibute (value should be"
-             "NXdetector) or from instrument group child structure.",
+        "try to deduce them from NX_class attibute (value should be"
+        "NXdetector) or from instrument group child structure.",
     )
     parser.add_argument(
         "--rot_angle_keys",
@@ -255,10 +256,10 @@ def main(argv):
         default=None,
         nargs="*",
         help="Allow manual definition of some parameters. "
-             "Valid parameters (and expected input unit) "
-             "are: {}. Should be added at the end of the command line because "
-             "will try to cover all text set after this "
-             "option.".format(_getPossibleInputParams()),
+        "Valid parameters (and expected input unit) "
+        "are: {}. Should be added at the end of the command line because "
+        "will try to cover all text set after this "
+        "option.".format(_getPossibleInputParams()),
     )
 
     parser.add_argument(
@@ -268,7 +269,7 @@ def main(argv):
         "--configuration-file",
         default=None,
         help="file containing the full configuration to convert from h5 "
-             "bliss to nexus",
+        "bliss to nexus",
     )
     options = parser.parse_args(argv[1:])
     if options.request_input:
@@ -282,6 +283,7 @@ def main(argv):
         return
     else:
         configuration = configuration_handler.configuration
+        assert isinstance(configuration, XRD3DHDF5Config)
         for title in configuration.init_titles:
             assert title != ""
         configuration.format = Format.XRD_3D

nxtomomill/converter/hdf5/acquisition/standardacquisition.py

@@ -107,6 +107,7 @@ class StandardAcquisition(BaseAcquisition):
         self._acq_expo_time = None
         self._copied_dataset = {}
         "register dataset copied. Key if the original location as" "DataUrl.path. Value is the DataUrl it has been moved to"
+        self._current_scan_n_frame = None
 
     @property
     def image_key(self):
@@ -284,7 +285,7 @@ class StandardAcquisition(BaseAcquisition):
         self._virtual_sources_len.append(n_frame)
         return n_frame
 
-    def __treate_valid_camera(
+    def _treate_valid_camera(
         self,
         detector_node,
         entry,
@@ -388,6 +389,7 @@ class StandardAcquisition(BaseAcquisition):
                     n_frame=n_frame,
                 )
             )
+        self._current_scan_n_frame = n_frame
 
     def camera_is_valid(self, det_name):
         assert isinstance(det_name, str)
@@ -449,7 +451,7 @@ class StandardAcquisition(BaseAcquisition):
                         continue
                     else:
                         detector_node = instrument_grp[key]
-                        self.__treate_valid_camera(
+                        self._treate_valid_camera(
                             detector_node,
                             entry=entry,
                             frame_type=type_,

nxtomomill/converter/hdf5/acquisition/xrd3dacquisition.py

@@ -38,6 +38,9 @@ __date__ = "19/04/2021"
 from nxtomomill.converter.hdf5.acquisition.standardacquisition import (
     StandardAcquisition,
 )
+import logging
+
+_logger = logging.getLogger(__name__)
 
 
 class XRD3DAcquisition(StandardAcquisition):
@@ -63,12 +66,52 @@ class XRD3DAcquisition(StandardAcquisition):
         self._rocking = rocking
 
     def _get_rocking_dataset(self, entry, n_frames):
-        raise NotImplementedError()
+        for grp in self._get_positioners_node(entry), entry:
+            try:
+                rocking, unit = self._get_node_values_for_frame_array(
+                    node=grp,
+                    n_frame=n_frames,
+                    keys=self.configuration.rocking_keys,
+                    info_retrieve="rocking",
+                    expected_unit=None,
+                )
+            except (ValueError, KeyError):
+                pass
+            else:
+                return rocking, None
+
+        mess = "Unable to find rocking for {}" "".format(self.root_url.path())
+        if self.raise_error_if_issue:
+            raise ValueError(mess)
+        else:
+            mess += "default value will be set. (0)"
+            _logger.warning(mess)
+            return 0, None
 
     def _get_base_tilt_dataset(self, entry, n_frames):
-        raise NotImplementedError()
+        for grp in self._get_positioners_node(entry), entry:
+            try:
+                base_tilt, unit = self._get_node_values_for_frame_array(
+                    node=grp,
+                    n_frame=n_frames,
+                    keys=self.configuration.base_tilt_keys,
+                    info_retrieve="base tilt",
+                    expected_unit=None,
+                )
+            except (ValueError, KeyError):
+                pass
+            else:
+                return base_tilt, None
+
+        mess = "Unable to find base tilt for {}" "".format(self.root_url.path())
+        if self.raise_error_if_issue:
+            raise ValueError(mess)
+        else:
+            mess += "default value will be set. (0)"
+            _logger.warning(mess)
+            return 0, None
 
-    def __treate_valid_camera(
+    def _treate_valid_camera(
         self,
         detector_node,
         entry,
@@ -78,7 +121,7 @@ class XRD3DAcquisition(StandardAcquisition):
         entry_path,
         entry_url,
     ):
-        super().__treate_valid_camera(
+        super()._treate_valid_camera(
             detector_node=detector_node,
             entry=entry,
             frame_type=frame_type,
@@ -89,17 +132,30 @@ class XRD3DAcquisition(StandardAcquisition):
         )
         # store base tilt information
         if not self._ignore_sample_output("base_tilt"):
-            rots = self._get_base_tilt_dataset(entry=entry, n_frames=self._n_frames)[0]
-            self._base_tilt.extend(rots)
+            base_tilt, _ = self._get_base_tilt_dataset(
+                entry=entry, n_frames=self._current_scan_n_frame
+            )
+            self._base_tilt.extend(base_tilt)
         else:
             self._base_tilt = None
+        # store rocking information
+        if not self._ignore_sample_output("rocking"):
+            rocking, _ = self._get_rocking_dataset(
+                entry=entry, n_frames=self._current_scan_n_frame
+            )
+            self._rocking.extend(rocking)
+        else:
+            self._rocking = None
 
     def _preprocess_registered_entries(self, output_file):
-        super()._preprocess_registered_entries(output_file=output_file)
         self._base_tilt = []
         self._rocking = []
+        super()._preprocess_registered_entries(output_file=output_file)
 
-    def _write_instrument(self, root_node):
-        super()._write_instrument(root_node)
-        #instrument_node = root_node.create_group("instrument")
-        #raise NotImplementedError()
+    def _write_sample(self, root_node):
+        super()._write_sample(root_node)
+        sample_node = root_node.require_group("sample")
+        if self._rocking is not None:
+            sample_node["rocking"] = self._rocking
+        if self._base_tilt is not None:
+            sample_node["base_tilt"] = self._base_tilt

nxtomomill/io/config.py

@@ -1106,6 +1106,49 @@ class TomoHDF5Config:
 class XRD3DHDF5Config(TomoHDF5Config):
     def __init__(self, *args, **kwargs):
         super().__init__(*args, **kwargs)
+        self._rocking_keys = settings.XRD3D.H5.ROCKING_KEYS
+        self._base_tilt_keys = settings.XRD3D.H5.BASE_TILT_KEYS
+
+    @property
+    def rocking_keys(self) -> Iterable:
+        return self._rocking_keys
+
+    @rocking_keys.setter
+    def rocking_keys(self, keys) -> None:
+        if not isinstance(keys, Iterable):
+            raise TypeError("'keys' should be an Iterable")
+        else:
+            self._rocking_keys = keys
+
+    @staticmethod
+    def from_cfg_file(file_path: str, encoding=None):
+        assert file_path is not None, "file_path should not be None"
+        config_parser = configparser.ConfigParser(allow_no_value=True)
+        config_parser.read(file_path, encoding=encoding)
+        return XRD3DHDF5Config.from_dict(config_parser)
+
+    @staticmethod
+    def from_dict(dict_: dict):
+        """
+        Create a HDF5Config object and set it from values contained in the
+        dictionary
+        :param dict dict_: settings dictionary
+        :return: HDF5Config
+        """
+        config = XRD3DHDF5Config()
+        config.load_from_dict(dict_)
+        return config
+
+    @property
+    def base_tilt_keys(self) -> Iterable:
+        return self._base_tilt_keys
+
+    @base_tilt_keys.setter
+    def base_tilt_keys(self, keys) -> None:
+        if not isinstance(keys, Iterable):
+            raise TypeError("'keys' should be an Iterable")
+        else:
+            self._base_tilt_keys = keys
 
 
 def generate_default_h5_config() -> dict:

nxtomomill/io/confighandler.py

@@ -191,6 +191,7 @@ class _BaseHDF5ConfigHandler:
 
 class TomoHDF5ConfigHandler(_BaseHDF5ConfigHandler):
     def _create_HDF5_config(self):
+        print("A")
         if self.argparse_options.config:
             return TomoHDF5Config.from_cfg_file(self.argparse_options.config)
         else:
@@ -296,8 +297,10 @@ class TomoHDF5ConfigHandler(_BaseHDF5ConfigHandler):
                     _logger.error(err)
                 return False
 
+
 class XRD3DHDF5ConfigHandler(_BaseHDF5ConfigHandler):
     def _create_HDF5_config(self):
+        print("B")
         if self.argparse_options.config:
             return XRD3DHDF5Config.from_cfg_file(self.argparse_options.config)
         else:
@@ -324,16 +327,13 @@ class XRD3DHDF5ConfigHandler(_BaseHDF5ConfigHandler):
             "x_trans_keys": ("x_trans_keys", self.get_tuple_of_keys_from_cmd),
             "y_trans_keys": ("y_trans_keys", self.get_tuple_of_keys_from_cmd),
             "z_trans_keys": ("z_trans_keys", self.get_tuple_of_keys_from_cmd),
-            "rot_angle_keys": (
-            "rotation_angle_keys", self.get_tuple_of_keys_from_cmd),
+            "rot_angle_keys": ("rotation_angle_keys", self.get_tuple_of_keys_from_cmd),
             "acq_expo_time_keys": (
                 "exposition_time_keys",
                 self.get_tuple_of_keys_from_cmd,
             ),
-            "x_pixel_size_key": (
-            "x_pixel_size_paths", self.get_tuple_of_keys_from_cmd),
-            "y_pixel_size_key": (
-            "y_pixel_size_paths", self.get_tuple_of_keys_from_cmd),
+            "x_pixel_size_key": ("x_pixel_size_paths", self.get_tuple_of_keys_from_cmd),
+            "y_pixel_size_key": ("y_pixel_size_paths", self.get_tuple_of_keys_from_cmd),
             "init_titles": ("init_titles", self.get_tuple_of_keys_from_cmd),
             "init_zserie_titles": (
                 "zserie_init_titles",
@@ -341,10 +341,8 @@ class XRD3DHDF5ConfigHandler(_BaseHDF5ConfigHandler):
             ),
             "dark_titles": ("dark_titles", self.get_tuple_of_keys_from_cmd),
             "ref_titles": ("flat_titles", self.get_tuple_of_keys_from_cmd),
-            "proj_titles": (
-            "projections_titles", self.get_tuple_of_keys_from_cmd),
-            "align_titles": (
-            "alignment_titles", self.get_tuple_of_keys_from_cmd),
+            "proj_titles": ("projections_titles", self.get_tuple_of_keys_from_cmd),
+            "align_titles": ("alignment_titles", self.get_tuple_of_keys_from_cmd),
             "set_params": ("param_already_defined", _extract_param_value),
         }
         for argparse_name, (config_name, format_fct) in mapping.items():
@@ -368,31 +366,31 @@ class XRD3DHDF5ConfigHandler(_BaseHDF5ConfigHandler):
             # check no other option are provided
             duplicated_inputs = []
             for opt in (
-                    "set_params",
-                    "align_titles",
-                    "proj_titles",
-                    "ref_titles",
-                    "dark_titles",
-                    "init_zserie_titles",
-                    "init_titles",
-                    "init_zserie_titles",
-                    "x_pixel_size_key",
-                    "y_pixel_size_key",
-                    "acq_expo_time_keys",
-                    "rot_angle_keys",
-                    "valid_camera_names",
-                    "z_trans_keys",
-                    "y_trans_keys",
-                    "x_trans_keys",
-                    "request_input",
-                    "raises_error",
-                    "ignore_sub_entries",
-                    "entries",
-                    "debug",
-                    "overwrite",
-                    "single_file",
-                    "file_extension",
-                    "field_of_view",
+                "set_params",
+                "align_titles",
+                "proj_titles",
+                "ref_titles",
+                "dark_titles",
+                "init_zserie_titles",
+                "init_titles",
+                "init_zserie_titles",
+                "x_pixel_size_key",
+                "y_pixel_size_key",
+                "acq_expo_time_keys",
+                "rot_angle_keys",
+                "valid_camera_names",
+                "z_trans_keys",
+                "y_trans_keys",
+                "x_trans_keys",
+                "request_input",
+                "raises_error",
+                "ignore_sub_entries",
+                "entries",
+                "debug",
+                "overwrite",
+                "single_file",
+                "file_extension",
+                "field_of_view",
             ):
                 if getattr(options, opt):
                     duplicated_inputs.append(opt)

nxtomomill/settings.py

@@ -140,6 +140,6 @@ class Tomo:
 
 class XRD3D(Tomo):
     class H5(Tomo.H5):
-        ROCKING_KEYS = ("mcha4_raw",)
+        ROCKING_KEYS = ("nfdtx",)
 
-        BASE_TILT_KEYS = ("mcha5_raw",)
+        BASE_TILT_KEYS = ("ffdtilt",)