linting, styling, mypying

FAIRmat-NFDI · Dec 11, 2023 · 5aa9977 · 5aa9977
1 parent 99d55ba
commit 5aa9977
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Showing 3 changed files with 188 additions and 188 deletions.
diff --git a/pynxtools/dataconverter/readers/em/reader.py b/pynxtools/dataconverter/readers/em/reader.py
@@ -17,14 +17,14 @@
 #
 """Parser for loading generic orientation microscopy data based on ."""
 
-# pylint: disable=no-member
+# pylint: disable=no-member,fixme
 
 from typing import Tuple, Any
 
 from pynxtools.dataconverter.readers.base.reader import BaseReader
 from pynxtools.dataconverter.readers.em.concepts.nexus_concepts import NxEmAppDef
 # from pynxtools.dataconverter.readers.em.subparsers.nxs_mtex import NxEmNxsMTexSubParser
-from pynxtools.dataconverter.readers.em.subparsers.nxs_pyxem import NxEmNxsPyxemSubParser
+# from pynxtools.dataconverter.readers.em.subparsers.nxs_pyxem import NxEmNxsPyxemSubParser
 from pynxtools.dataconverter.readers.em.subparsers.nxs_imgs import NxEmImagesSubParser
 from pynxtools.dataconverter.readers.em.utils.default_plots import NxEmDefaultPlotResolver
 # from pynxtools.dataconverter.readers.em.geometry.convention_mapper import NxEmConventionMapper
@@ -126,7 +126,7 @@ def read(self,
         # sub_parser = "image_tiff"
         subparser = NxEmImagesSubParser(entry_id, file_paths[0])
         subparser.parse(template)
-        
+
         # for dat_instance in case.dat_parser_type:
         #     print(f"Process pieces of information in {dat_instance} tech partner file...")
         #    continue
@@ -146,7 +146,7 @@ def read(self,
         # 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)
-        
+
         if True is False:
             nxs_plt = NxEmDefaultPlotResolver()
             # if nxs_mtex is the sub-parser

diff --git a/pynxtools/dataconverter/readers/em/subparsers/image_tiff_tfs.py b/pynxtools/dataconverter/readers/em/subparsers/image_tiff_tfs.py
@@ -94,7 +94,7 @@ def get_metadata(self):
             sequence = []  # decide I/O order in which metadata for childs of parent concepts will be read
             for key, value in tfs_parent_concepts_byte_offset.items():
                 if value is not None:
-                    sequence.append((key, value)) 
+                    sequence.append((key, value))
                     # tuple of parent_concept name and byte offset
             sequence = sort_ascendingly_by_second_argument(sequence)
             print(sequence)
@@ -131,7 +131,7 @@ def get_metadata(self):
                                 else:
                                     self.tmp["meta"][f"{parent}/{term}"] = value
                         else:
-                            raise ValueError(f"Detected an unexpected case {parent}/{term}, type: {type(value)} !")                
+                            raise ValueError(f"Detected an unexpected case {parent}/{term}, type: {type(value)} !")
                     else:
                         pass
 
@@ -149,7 +149,7 @@ def process_into_template(self, template: dict) -> dict:
             self.process_event_data_em_metadata(template)
             self.process_event_data_em_data(template)
         return template
-    
+
     def process_event_data_em_data(self, template: dict) -> dict:
         """Add respective heavy data."""
         # default display of the image(s) representing the data collected in this event
@@ -167,8 +167,8 @@ def process_event_data_em_data(self, template: dict) -> dict:
             # explorative viewing using H5Web than what traditionally typical image viewers are meant for
             image_identifier = 1
             trg = f"/ENTRY[entry{self.entry_id}]/measurement/EVENT_DATA_EM_SET[event_data_em_set]/" \
-                    f"EVENT_DATA_EM[event_data_em{self.event_id}]/" \
-                    f"IMAGE_R_SET[image_r_set{image_identifier}]/DATA[image]"
+                  f"EVENT_DATA_EM[event_data_em{self.event_id}]/" \
+                  f"IMAGE_R_SET[image_r_set{image_identifier}]/DATA[image]"
             # TODO::writer should decorate automatically!
             template[f"{trg}/title"] = f"Image"
             template[f"{trg}/@NX_class"] = f"NXdata"  # TODO::writer should decorate automatically!
@@ -183,8 +183,8 @@ def process_event_data_em_data(self, template: dict) -> dict:
                 template[f"{trg}/@axes"].append(f"axis_{dim}")
             template[f"{trg}/intensity"] = {"compress": np.array(fp), "strength": 1}
             #  0 is y while 1 is x for 2d, 0 is z, 1 is y, while 2 is x for 3d
-            template[f"{trg}/intensity/@long_name"] = f"Signal"         
-    
+            template[f"{trg}/intensity/@long_name"] = f"Signal"
+
             sxy = {"x": self.tmp["meta"]["EScan/PixelWidth"],
                    "y": self.tmp["meta"]["EScan/PixelHeight"]}
             shp = np.shape(np.array(fp))
@@ -206,14 +206,14 @@ def process_event_data_em_data(self, template: dict) -> dict:
             for dim in dims:
                 template[f"{trg}/AXISNAME[axis_{dim}]"] \
                     = {"compress": np.asarray(np.linspace(0,
-                                                            nxy[dim] - 1,
-                                                            num=nxy[dim],
-                                                            endpoint=True) * sxy[dim], np.float64), "strength": 1}
+                                                          nxy[dim] - 1,
+                                                          num=nxy[dim],
+                                                          endpoint=True) * sxy[dim], np.float64), "strength": 1}
                 template[f"{trg}/AXISNAME[axis_{dim}]/@long_name"] \
                     = f"Coordinate along {dim}-axis ({scan_unit[dim]})"
                 template[f"{trg}/AXISNAME[axis_{dim}]/@units"] = f"{scan_unit[dim]}"
         return template
-    
+
     def process_event_data_em_metadata(self, template: dict) -> dict:
         """Add respective metadata."""
         # contextualization to understand how the image relates to the EM session