Deprecated the phrasing SubParser in favour for parser, aligning name…

…s of src code directories

src/pynxtools_em/config/image_png_protochips_cfg.py → src/pynxtools_em/configurations/image_png_protochips_cfg.py

@@ -15,7 +15,7 @@
 # See the License for the specific language governing permissions and
 # limitations under the License.
 #
-"""Configuration of the image_png_protochips subparser."""
+"""Configuration of the image_png_protochips parser."""
 
 import re
 from typing import Dict

src/pynxtools_em/config/image_tiff_tfs_cfg.py → src/pynxtools_em/configurations/image_tiff_tfs_cfg.py

@@ -15,7 +15,7 @@
 # See the License for the specific language governing permissions and
 # limitations under the License.
 #
-"""Configuration of the image_tiff_tfs subparser."""
+"""Configuration of the image_tiff_tfs parser."""
 
 from numpy import pi
 

src/pynxtools_em/config/rsciio_velox_cfg.py → src/pynxtools_em/configurations/rsciio_velox_cfg.py

@@ -17,7 +17,7 @@
 #
 """Map content from Velox EMD file format onto NeXus concepts.
 
-# TODO move to pynxtools-em Velox subparser documentation
+# TODO move to pynxtools-em Velox parser documentation
 "Core/MetadataDefinitionVersion": ["7.9"]
 "Core/MetadataSchemaVersion": ["v1/2013/07"]
 all *.emd files from https://ac.archive.fhi.mpg.de/D62142 parsed with

src/pynxtools_em/subparsers/convention_reader.py → src/pynxtools_em/parsers/convention_reader.py

@@ -21,26 +21,25 @@
 
 import flatdict as fd
 import yaml
-
 from pynxtools_em.concepts.mapping_functors import (
     add_specific_metadata,
     variadic_path_to_specific_path,
 )
-from pynxtools_em.config.conventions_cfg import (
+from pynxtools_em.configurations.conventions_cfg import (
     DETECTOR_CSYS_TO_NEXUS,
     GNOMONIC_CSYS_TO_NEXUS,
     PATTERN_CSYS_TO_NEXUS,
     PROCESSING_CSYS_TO_NEXUS,
     ROTATIONS_TO_NEXUS,
     SAMPLE_CSYS_TO_NEXUS,
 )
-from pynxtools_em.geometry.euler_angle_convention import euler_convention
-from pynxtools_em.geometry.handed_cartesian import (
+from pynxtools_em.geometries.euler_angle_convention import euler_convention
+from pynxtools_em.geometries.handed_cartesian import (
     AXIS_DIRECTIONS,
     REFERENCE_FRAMES,
     is_cartesian_cs_well_defined,
 )
-from pynxtools_em.geometry.msmse_convention import is_consistent_with_msmse_convention
+from pynxtools_em.geometries.msmse_convention import is_consistent_with_msmse_convention
 
 
 class NxEmConventionParser:

src/pynxtools_em/subparsers/hfive_apex.py → src/pynxtools_em/parsers/hfive_apex.py

@@ -23,7 +23,6 @@
 import numpy as np
 from diffpy.structure import Lattice, Structure
 from orix.quaternion import Orientation
-
 from pynxtools_em.concepts.nxs_em_eds_indexing import NxEmEdsIndexing
 from pynxtools_em.concepts.nxs_image_r_set import NxImageRealSpaceSet
 from pynxtools_em.concepts.nxs_object import NxObject
@@ -35,7 +34,7 @@
     REGULAR_TILING,
     SQUARE_TILING,
 )
-from pynxtools_em.subparsers.hfive_base import HdfFiveBaseParser
+from pynxtools_em.parsers.hfive_base import HdfFiveBaseParser
 from pynxtools_em.utils.get_scan_points import get_scan_point_coords
 from pynxtools_em.utils.get_xrayline_iupac_names import get_xrayline_candidates
 from pynxtools_em.utils.hfive_utils import read_strings_from_dataset
@@ -376,7 +375,7 @@ def parse_and_normalize_group_ebsd_data(self, fp, ckey: str):
         # distances for hexagonal or square tiling of R^2
         # self.tmp[ckey]["grid_type"] in ["HexGrid", "SqrGrid"]:
         # if just SQUARE_GRID there is no point to explicitly compute the scan_point
-        # coordinates here (for every subparser) especially not when the respective
+        # coordinates here (for every parser) especially not when the respective
         # quantity from the tech partner is just a pixel index i.e. zeroth, first px ...
         # however, ideally the tech partners would use the scan_point fields to report
         # calibrated absolute scan point positions in the local reference frame of the

src/pynxtools_em/subparsers/hfive_base.py → src/pynxtools_em/parsers/hfive_base.py

@@ -17,16 +17,16 @@
 #
 """Parent class for all tech partner-specific HDF5 parsers for mapping on NXem."""
 
-import numpy as np
-import h5py
 from typing import Dict, List
 
-from pynxtools_em.subparsers.hfive_concept import (
-    IS_GROUP,
-    IS_REGULAR_DATASET,
-    IS_COMPOUND_DATASET,
+import h5py
+import numpy as np
+from pynxtools_em.parsers.hfive_concept import (
     IS_ATTRIBUTE,
+    IS_COMPOUND_DATASET,
     IS_FIELD_IN_COMPOUND_DATASET,
+    IS_GROUP,
+    IS_REGULAR_DATASET,
     Concept,
 )
 
@@ -437,7 +437,7 @@ def get_value(self, h5path):
 # with which the content in the HDF5 file is formatted
 # Therefore, at least some of the content and how that content is
 # formatted is inspected to make an informed decision which specific hfive
-# subparser can be expected to deal at all with the content of the HDF5 file
+# parser can be expected to deal at all with the content of the HDF5 file
 
 # For the example of EBSD there was once a suggestion made by the academic community
 # to report EBSD results via HDF5, specifically via H5EBSD (Jackson et al.).

src/pynxtools_em/subparsers/hfive_bruker.py → src/pynxtools_em/parsers/hfive_bruker.py

@@ -22,14 +22,13 @@
 import h5py
 import numpy as np
 from diffpy.structure import Lattice, Structure
-
 from pynxtools_em.examples.ebsd_database import (
     ASSUME_PHASE_NAME_TO_SPACE_GROUP,
     FLIGHT_PLAN,
     REGULAR_TILING,
     SQUARE_TILING,
 )
-from pynxtools_em.subparsers.hfive_base import HdfFiveBaseParser
+from pynxtools_em.parsers.hfive_base import HdfFiveBaseParser
 
 # HEXAGONAL_GRID
 from pynxtools_em.utils.get_scan_points import get_scan_point_coords

src/pynxtools_em/subparsers/hfive_dreamthreed.py → src/pynxtools_em/parsers/hfive_dreamthreed.py

@@ -28,7 +28,7 @@
     REGULAR_TILING,
     SQUARE_TILING,
 )
-from pynxtools_em.subparsers.hfive_base import HdfFiveBaseParser
+from pynxtools_em.parsers.hfive_base import HdfFiveBaseParser
 from pynxtools_em.utils.hfive_utils import (
     read_strings_from_dataset,
 )

src/pynxtools_em/subparsers/hfive_ebsd.py → src/pynxtools_em/parsers/hfive_ebsd.py

@@ -22,14 +22,13 @@
 import h5py
 import numpy as np
 from diffpy.structure import Lattice, Structure
-
 from pynxtools_em.examples.ebsd_database import (
     ASSUME_PHASE_NAME_TO_SPACE_GROUP,
     FLIGHT_PLAN,
     REGULAR_TILING,
     SQUARE_TILING,
 )
-from pynxtools_em.subparsers.hfive_base import HdfFiveBaseParser
+from pynxtools_em.parsers.hfive_base import HdfFiveBaseParser
 
 # HEXAGONAL_GRID
 from pynxtools_em.utils.get_scan_points import get_scan_point_coords

src/pynxtools_em/subparsers/hfive_edax.py → src/pynxtools_em/parsers/hfive_edax.py

@@ -22,15 +22,14 @@
 import h5py
 import numpy as np
 from diffpy.structure import Lattice, Structure
-
 from pynxtools_em.examples.ebsd_database import (
     ASSUME_PHASE_NAME_TO_SPACE_GROUP,
     FLIGHT_PLAN,
     HEXAGONAL_FLAT_TOP_TILING,
     REGULAR_TILING,
     SQUARE_TILING,
 )
-from pynxtools_em.subparsers.hfive_base import HdfFiveBaseParser
+from pynxtools_em.parsers.hfive_base import HdfFiveBaseParser
 from pynxtools_em.utils.hfive_utils import (
     EULER_SPACE_SYMMETRY,
     format_euler_parameterization,

src/pynxtools_em/subparsers/hfive_emsoft.py → src/pynxtools_em/parsers/hfive_emsoft.py

@@ -17,11 +17,11 @@
 #
 """(Sub-)parser mapping concepts and content from Marc deGraeff's EMsoft *.h5 files on NXem."""
 
-import numpy as np
-import h5py
 from typing import Dict
 
-from pynxtools_em.subparsers.hfive_base import HdfFiveBaseParser
+import h5py
+import numpy as np
+from pynxtools_em.parsers.hfive_base import HdfFiveBaseParser
 from pynxtools_em.utils.hfive_utils import read_strings_from_dataset
 
 

src/pynxtools_em/subparsers/hfive_oxford.py → src/pynxtools_em/parsers/hfive_oxford.py

@@ -22,13 +22,12 @@
 import h5py
 import numpy as np
 from diffpy.structure import Lattice, Structure
-
 from pynxtools_em.examples.ebsd_database import (
     FLIGHT_PLAN,
     REGULAR_TILING,
     SQUARE_TILING,
 )
-from pynxtools_em.subparsers.hfive_base import HdfFiveBaseParser
+from pynxtools_em.parsers.hfive_base import HdfFiveBaseParser
 from pynxtools_em.utils.hfive_utils import (
     format_euler_parameterization,
     read_strings_from_dataset,

src/pynxtools_em/subparsers/image_png_protochips.py → src/pynxtools_em/parsers/image_png_protochips.py

@@ -27,12 +27,11 @@
 import numpy as np
 import xmltodict
 from PIL import Image
-
 from pynxtools_em.concepts.mapping_functors import (
     add_specific_metadata,
     variadic_path_to_specific_path,
 )
-from pynxtools_em.config.image_png_protochips_cfg import (
+from pynxtools_em.configurations.image_png_protochips_cfg import (
     AXON_AUX_DYNAMIC_TO_NX_EM,
     AXON_CHIP_DYNAMIC_TO_NX_EM,
     AXON_DETECTOR_STATIC_TO_NX_EM,
@@ -41,7 +40,7 @@
     AXON_VARIOUS_DYNAMIC_TO_NX_EM,
     specific_to_variadic,
 )
-from pynxtools_em.subparsers.image_base import ImgsBaseParser
+from pynxtools_em.parsers.image_base import ImgsBaseParser
 from pynxtools_em.utils.get_file_checksum import (
     DEFAULT_CHECKSUM_ALGORITHM,
     get_sha256_of_file_content,
@@ -50,7 +49,7 @@
 from pynxtools_em.utils.xml_utils import flatten_xml_to_dict
 
 
-class ProtochipsPngSetSubParser(ImgsBaseParser):
+class ProtochipsPngSetParser(ImgsBaseParser):
     def __init__(self, file_path: str = "", entry_id: int = 1, verbose: bool = False):
         super().__init__(file_path)
         self.entry_id = entry_id

src/pynxtools_em/subparsers/image_tiff.py → src/pynxtools_em/parsers/image_tiff.py

@@ -15,17 +15,17 @@
 # See the License for the specific language governing permissions and
 # limitations under the License.
 #
-"""Derived image class to derive every tech-partner-specific TIFF subparser from."""
+"""Derived image class to derive every tech-partner-specific TIFF parser from."""
 
 import mmap
 from typing import Dict
+
 from PIL import Image
 from PIL.TiffTags import TAGS
-
-from pynxtools_em.subparsers.image_base import ImgsBaseParser
+from pynxtools_em.parsers.image_base import ImgsBaseParser
 
 
-class TiffSubParser(ImgsBaseParser):
+class TiffParser(ImgsBaseParser):
     """Read Tagged Image File Format TIF/TIFF."""
 
     def __init__(self, file_path: str = ""):
@@ -93,7 +93,7 @@ def get_tags(self, verbose: bool = False):
     def parse_and_normalize(self):
         """Perform actual parsing filling cache self.tmp."""
         if self.supported is True:
-            print(f"Parsing via TiffSubParser...")
+            print(f"Parsing via TiffParser...")
             self.get_tags()
         else:
             print(f"{self.file_path} is not a TIFF file this parser can process !")

src/pynxtools_em/subparsers/image_tiff_tfs.py → src/pynxtools_em/parsers/image_tiff_tfs.py

@@ -24,9 +24,8 @@
 import numpy as np
 from PIL import Image
 from PIL.TiffTags import TAGS
-
 from pynxtools_em.concepts.mapping_functors import add_specific_metadata
-from pynxtools_em.config.image_tiff_tfs_cfg import (
+from pynxtools_em.configurations.image_tiff_tfs_cfg import (
     TFS_APERTURE_STATIC_TO_NX_EM,
     TFS_DETECTOR_STATIC_TO_NX_EM,
     TFS_OPTICS_DYNAMIC_TO_NX_EM,
@@ -35,8 +34,8 @@
     TFS_VARIOUS_DYNAMIC_TO_NX_EM,
     TFS_VARIOUS_STATIC_TO_NX_EM,
 )
-from pynxtools_em.subparsers.image_tiff import TiffSubParser
-from pynxtools_em.subparsers.image_tiff_tfs_concepts import (
+from pynxtools_em.parsers.image_tiff import TiffParser
+from pynxtools_em.parsers.image_tiff_tfs_concepts import (
     get_fei_childs,
     get_fei_parent_concepts,
 )
@@ -46,7 +45,7 @@
 )
 
 
-class TfsTiffSubParser(TiffSubParser):
+class TfsTiffParser(TiffParser):
     def __init__(self, file_path: str = "", entry_id: int = 1):
         super().__init__(file_path)
         self.entry_id = entry_id

src/pynxtools_em/subparsers/image_tiff_tfs_concepts.py → src/pynxtools_em/parsers/image_tiff_tfs_concepts.py

@@ -15,11 +15,10 @@
 # See the License for the specific language governing permissions and
 # limitations under the License.
 #
-"""Configuration of the image_tiff_tfs subparser."""
+"""Configuration of the image_tiff_tfs parser."""
 
 from typing import List
 
-
 # this example exemplifies the situation for the TFS/FEI SEM Apreo from the IKZ of Prof. Martin Albrecht
 # thanks to Robert Kernke it was clarified the microscope has several detectors and imaging modes
 # these imaging modes control the specific TFS/FEI concept instances stored in the respective TIFF file

src/pynxtools_em/subparsers/nxs_imgs.py → src/pynxtools_em/parsers/nxs_imgs.py

@@ -17,11 +17,11 @@
 #
 """Parser mapping content of specific image files on NeXus."""
 
-from pynxtools_em.subparsers.image_tiff_tfs import TfsTiffSubParser
-from pynxtools_em.subparsers.image_png_protochips import ProtochipsPngSetSubParser
+from pynxtools_em.parsers.image_png_protochips import ProtochipsPngSetParser
+from pynxtools_em.parsers.image_tiff_tfs import TfsTiffParser
 
 
-class NxEmImagesSubParser:
+class NxEmImagesParser:
     """Map content from different type of image files on an instance of NXem."""
 
     def __init__(self, entry_id: int = 1, file_path: str = "", verbose: bool = False):
@@ -35,12 +35,12 @@ def __init__(self, entry_id: int = 1, file_path: str = "", verbose: bool = False
         self.verbose = verbose
 
     def identify_image_type(self):
-        """Identify if image matches known mime type and has content for which subparser exists."""
+        """Identify if image matches known mime type and has content for which parser exists."""
         # tech partner formats used for measurement
-        img = TfsTiffSubParser(self.file_path)
+        img = TfsTiffParser(self.file_path)
         if img.supported:
             return "single_tiff_tfs"
-        img = ProtochipsPngSetSubParser(self.file_path)
+        img = ProtochipsPngSetParser(self.file_path)
         if img.supported:
             return "set_of_zipped_png_protochips"
         return None
@@ -54,13 +54,13 @@ def parse(self, template: dict) -> dict:
             return template
         print(f"{self.__class__.__name__} identified content as {image_parser_type}")
         # see also comments for respective nxs_pyxem parser
-        # and its interaction with tech-partner-specific hfive_* subparsers
+        # and its interaction with tech-partner-specific hfive_* parsers
         if image_parser_type == "single_tiff_tfs":
-            tiff = TfsTiffSubParser(self.file_path, self.entry_id)
+            tiff = TfsTiffParser(self.file_path, self.entry_id)
             tiff.parse_and_normalize()
             tiff.process_into_template(template)
         elif image_parser_type == "set_of_zipped_png_protochips":
-            pngs = ProtochipsPngSetSubParser(self.file_path, self.entry_id)
+            pngs = ProtochipsPngSetParser(self.file_path, self.entry_id)
             pngs.parse_and_normalize()
             pngs.process_into_template(template)
         # add here further specific content (sub-)parsers for formats from other

src/pynxtools_em/subparsers/nxs_mtex.py → src/pynxtools_em/parsers/nxs_mtex.py

@@ -47,7 +47,7 @@ def hfive_to_template(payload):
     return np.asarray(payload[...], dtype=payload.dtype)
 
 
-class NxEmNxsMTexSubParser:
+class NxEmNxsMTexParser:
     """Map content from *.nxs.mtex files on an instance of NXem."""
 
     def __init__(self, entry_id: int = 1, file_path: str = "", verbose: bool = False):

src/pynxtools_em/subparsers/nxs_nion.py → src/pynxtools_em/parsers/nxs_nion.py

@@ -45,7 +45,7 @@
 from pynxtools_em.utils.nion_utils import uuid_to_file_name
 
 
-class NionProjectSubParser:
+class NionProjectParser:
     """Parse (zip-compressed archive of a) nionswift project with its content."""
 
     def __init__(