Store initial work that it does not get lost but this is not even a d…

…raft

pynxtools/dataconverter/readers/em/reader.py

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+#
+# Copyright The NOMAD Authors.
+#
+# This file is part of NOMAD. See https://nomad-lab.eu for further info.
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+#     http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+#
+"""Parser for loading generic orientation microscopy data based on ."""
+
+# pylint: disable=no-member
+
+from typing import Tuple, Any
+
+from pynxtools.dataconverter.readers.base.reader import BaseReader
+
+"""
+from pynxtools.dataconverter.readers.em_om.utils.use_case_selector \
+    import EmOmUseCaseSelector
+
+from pynxtools.dataconverter.readers.em_om.utils.generic_eln_io \
+    import NxEmOmGenericElnSchemaParser
+
+from pynxtools.dataconverter.readers.em_om.utils.orix_ebsd_parser \
+    import NxEmOmOrixEbsdParser
+
+from pynxtools.dataconverter.readers.em_om.utils.mtex_ebsd_parser \
+    import NxEmOmMtexEbsdParser
+
+from pynxtools.dataconverter.readers.em_om.utils.zip_ebsd_parser \
+    import NxEmOmZipEbsdParser
+
+from pynxtools.dataconverter.readers.em_om.utils.dream3d_ebsd_parser \
+    import NxEmOmDreamThreedEbsdParser
+
+from pynxtools.dataconverter.readers.em_om.utils.em_nexus_plots \
+    import em_om_default_plot_generator"""
+
+
+class EmReader(BaseReader):
+    """Parse content from file formats of the electron microscopy community."""
+
+    # pylint: disable=too-few-public-methods
+
+    # Whitelist for the NXDLs that the reader supports and can process
+    supported_nxdls = ["NXem"]
+
+    # pylint: disable=duplicate-code
+    def read(self,
+             template: dict = None,
+             file_paths: Tuple[str] = None,
+             objects: Tuple[Any] = None) -> dict:
+        """Read data from given file, return filled template dictionary em."""
+        # pylint: disable=duplicate-code
+        template.clear()
+
+        # this em_om parser combines multiple sub-parsers
+        # so we need the following input:
+        # logical analysis which use case
+        # data input from an ELN (using an ELN-agnostic) YAML representation
+        # data input from technology partner files
+        # functionalities for creating default plots
+
+        entry_id = 1
+        # if len(file_paths) != 2:
+        #     print("Generation of example data not implemented yet...!")
+        #     return {}
+
+        print("Identify information sources (ELN, RDM config, tech files) to deal with...")
+        case = EmUseCaseSelector(file_paths)
+        if case.is_valid is False:
+            print("Such a combination of input (file) is not supported !")
+            return {}
+
+        print("Process pieces of information within RDM-specific ELN export file...")
+        if case.eln_parser_type == "oasis":
+            # pattern_simulation = False
+            # if case.dat_parser_type == "zip":
+            #     pattern_simulation = True
+            eln = OasisCustomSchemaInstanceFileParser(case.eln[0], entry_id)
+            eln.parse(template)
+        else:
+            print("No interpretable ELN input found!")
+
+        print("Process pieces of information in RDM-specific configuration files...")
+        if case.cfg_parser_type == "oasis":
+            cfg = OasisSpecificConfigInstanceFileParser(case.cfg[0], entry_id)
+            cfg.parse(template)
+        else:
+            print("No interpretable configuration file offered")
+
+        nxs = NxEmAppDefContent()
+        nxs.parse(template)
+
+        print("Parse and map pieces of information within files from tech partners...")
+        # for dat_instance in case.dat_parser_type:
+        #     print(f"Process pieces of information in {dat_instance} tech partner file...")
+        #    continue
+"""             if case.dat_parser_type == "orix":
+                orix_parser = NxEmOmOrixEbsdParser(case.dat[0], entry_id)
+                # h5oina parser evaluating content and plotting with orix on the fly
+                orix_parser.parse(template)
+            elif case.dat_parser_type == "mtex":
+                mtex_parser = NxEmOmMtexEbsdParser(case.dat[0], entry_id)
+                # ebsd parser because concept suggested for MTex by M. Kühbach
+                # would include different HDF5 dumps for different MTex classes
+                mtex_parser.parse(template)
+            elif case.dat_parser_type == "zip":
+                zip_parser = NxEmOmZipEbsdParser(case.dat[0], entry_id)
+                zip_parser.parse(template)
+            elif case.dat_parser_type == "dream3d":
+                dream_parser = NxEmOmDreamThreedEbsdParser(case.dat[0], entry_id)
+                dream_parser.parse(template)
+            # elif case.dat_parser_type == "kikuchipy":
+            # elif case.dat_parser_type == "pyxem":
+            # elif case.dat_parser_type == "score":
+            # elif case.dat_parser_type == "qube":
+            # elif case.dat_parser_type == "paradis":
+            # elif case.dat_parser_type == "brinckmann": """
+
+        # at this point the data for the default plots should already exist
+        # we only need to decorate the template to point to the mandatory ROI overview
+        # print("Create NeXus default plottable data...")
+        # em_default_plot_generator(template, 1)
+
+        debugging = False
+        if debugging is True:
+            print("Reporting state of template before passing to HDF5 writing...")
+            for keyword in template.keys():
+                print(keyword)
+                # print(type(template[keyword]))
+                # print(template[keyword])
+
+        print("Forward instantiated template to the NXS writer...")
+        return template
+
+
+# This has to be set to allow the convert script to use this reader.
+READER = EmReader