Apply assorted ruff rules #59

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DimitriPapadopoulos wants to merge 20 commits into lamyj:master from DimitriPapadopoulos:ruff

.ci/build/apt.py

            
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    @@ -1,6 +1,5 @@
  
    import os

    import subprocess

    import sys

    import tempfile

    import urllib.request

    @@ -14,16 +13,16 @@
  
    repository = "https://iris-packages.s3.unistra.fr"

    try:

       urllib.request.urlopen("{}/apt/dists/{}/Release".format(repository, codename))

       urllib.request.urlopen(f"{repository}/apt/dists/{codename}/Release")

    except urllib.request.HTTPError:

        pass

    else:

        with tempfile.NamedTemporaryFile() as fd:

            fd.write(urllib.request.urlopen("{}/gpg.key".format(repository)).read())

            fd.write(urllib.request.urlopen(f"{repository}/gpg.key").read())

            fd.flush()

            subprocess.check_call(["apt-key", "add", fd.name])

        subprocess.check_call([

            "add-apt-repository", "deb {}/apt {} main".format(repository, codename)])

            "add-apt-repository", f"deb {repository}/apt {codename} main"])

        subprocess.check_call(["apt-get", "update"])

    subprocess.check_call([

.ci/build/build.py

            
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    @@ -1,6 +1,4 @@
  
    import multiprocessing

    import os

    import re

    import subprocess

    import sys

    @@ -18,8 +16,8 @@
  
        [

            "cmake", 

            "-G", "Ninja",

            "-DPython_EXECUTABLE={}".format(sys.executable),

            "-DCMAKE_INSTALL_PREFIX={}".format(install_dir), 

            f"-DPython_EXECUTABLE={sys.executable}",

            f"-DCMAKE_INSTALL_PREFIX={install_dir}", 

            workspace],

        cwd=build_dir)

src/python/dicomifier/bruker_to_dicom/io/flat_dicom_writer.py

-Original file line number
+Diff line change
@@ Expand Up / @@ -26,7 +26,8 @@ def __call__(self, data_set): @@
                 os.makedirs(self.root)
             if self.iso_9660:
-                filename = "{:08d}.dcm".format(1+len(self.files))
+                count = 1 + len(self.files)
+                filename = f"{count:08}.dcm"
             else:
                 filename = data_set[odil.registry.SOPInstanceUID][0].decode()
@@ Expand Down @@

src/python/dicomifier/bruker_to_dicom/io/nested_dicom_writer.py

-Original file line number
+Diff line change
@@ Expand Up / @@ -30,7 +30,8 @@ def __call__(self, data_set): @@
             self._counts.setdefault(directory, 0)
             if self.iso_9660:
-                filename = "IM{:06d}".format(1+self._counts[directory])
+                count = 1 + self._counts[directory]
+                filename = f"IM{count:06}"
             else:
                 filename = data_set[odil.registry.SOPInstanceUID][0].decode()
@@ Expand Down @@

src/python/dicomifier/bruker_to_dicom/modules/image.py

            
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    @@ -108,7 +108,7 @@ def get_frame_index(generator, frame_index):
  
        contribution = [

            [fg[1], frame_index[i]]

            for i, fg in enumerate(generator.frame_groups) 

            if fg[1] != 'FG_SLICE']

            if fg[1] != "FG_SLICE"]

        return odil.DataSet(

            PurposeOfReferenceCodeSequence=[odil.DataSet(

src/python/dicomifier/commands/search.py

-Original file line number
+Diff line change
@@ Expand Up / @@ -44,9 +44,9 @@ def __init__(self, argument): @@
             else:
                 try:
                     tag = int(items[0], 16)
-                except ValueError:
+                except ValueError as e:
                     raise argparse.ArgumentTypeError(
-                        f"Invalid DICOM tag '{items[0]}'")
+                        f"Invalid DICOM tag '{items[0]}'") from e
                 else:
                     self.tag = odil.Tag(tag)
@@ Expand Down @@

src/python/dicomifier/dicom_to_nifti/convert.py

            
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    @@ -126,7 +126,7 @@ def __init__(self, data_set):
  
                self.prefix = "{}: ".format(" / ".join(elements))

            except Exception as e:

                logger.debug("Series context configuration error: \"%s\"", e)

                logger.debug('Series context configuration error: "%s"', e)

                self.prefix = ""

        def filter(self, record):

    @@ -215,11 +215,7 @@ def convert_series_data_sets(data_sets, dtype=None, extra_splitters=None):
  
            # Update progress information

            if len(stacks) > 1:

                stack_info = "{}/{}".format(1 + stack_index, len(stacks))

            else:

                stack_info = ""

            if stack_info:

                logger.debug("Converting stack %s", stack_info)

                logger.debug(f"Converting stack {1 + stack_index}/{len(stacks)}")

            sort(key, stack)

            nifti_meta_data = meta_data.get_meta_data(stack, meta_data_cache)

src/python/dicomifier/dicom_to_nifti/image.py

            
                      Original file line number
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                      Diff line change
                  
    @@ -9,7 +9,6 @@
  
    import math

    import re

    import nibabel

    import numpy

    import odil

    @@ -40,7 +39,7 @@ def get_slice_image(data_set, shape, cache=None):
  
                siemens_data = siemens.parse_csa(item.get_memory_view().tobytes())

                number_of_tiles = siemens_data["NumberOfImagesInMosaic"][0]

                tiles_per_line = int(math.ceil(math.sqrt(number_of_tiles)))

                tiles_per_line = math.ceil(math.sqrt(number_of_tiles))

                # Re-arrange array so that tiles are contiguous

                array = array.reshape(

    @@ -107,7 +106,7 @@ def get_shape(stack):
  
            siemens_data = siemens.parse_csa(item.get_memory_view().tobytes())

            number_of_tiles = siemens_data["NumberOfImagesInMosaic"][0]

            tiles_per_line = int(math.ceil(math.sqrt(number_of_tiles)))

            tiles_per_line = math.ceil(math.sqrt(number_of_tiles))

            rows = data_set[odil.registry.Rows][0] // tiles_per_line

            cols = data_set[odil.registry.Columns][0] // tiles_per_line

    @@ -311,7 +310,7 @@ def get_geometry(stack):
  
            siemens_data = siemens.parse_csa(item.get_memory_view().tobytes())

            number_of_tiles = siemens_data["NumberOfImagesInMosaic"][0]

            tiles_per_line = int(math.ceil(math.sqrt(number_of_tiles)))

            tiles_per_line = math.ceil(math.sqrt(number_of_tiles))

            # Get the origin of the tiles (i.e. origin of the first tile), cf.

            # http://nipy.org/nibabel/dicom/dicom_mosaic.html

src/python/dicomifier/dicom_to_nifti/io.py

            
                      Original file line number
                      Diff line number
                      Diff line change
                  
    @@ -62,16 +62,14 @@ def get_dicomdir_files(path):
  
        """ Return the list of files indexed in a DICOMDIR file.

        """

        dicom_files = []

        dicomdir = odil.Reader.read_file(path)[1]

        for record in dicomdir[odil.registry.DirectoryRecordSequence]:

            if record[odil.registry.DirectoryRecordType][0] == b"IMAGE":

                dicom_files.append(

                    os.path.join(

                        os.path.dirname(path),

                        *[x.decode() for x in record[odil.registry.ReferencedFileID]]))

        return dicom_files

        return [

    		os.path.join(

                os.path.dirname(path),

                *[x.decode() for x in record[odil.registry.ReferencedFileID]])

    		for record in dicomdir[odil.registry.DirectoryRecordSequence]

    		if record[odil.registry.DirectoryRecordType][0] == b"IMAGE"

        ]

    def write_nifti(nifti_data, destination, zip, series_directory=None):

        """ Write the NIfTI image and meta-data in the given destination.

    @@ -146,28 +144,28 @@ def get_first_item(item):
  
            # Patient directory: <PatientName> or <PatientID> or <StudyInstanceUID>.

            patient_directory = None

            if "PatientName" in meta_data and meta_data["PatientName"]:

            if meta_data.get("PatientName"):

                patient_directory = get_first_item(

                    meta_data["PatientName"])["Alphabetic"]

            elif "PatientID" in meta_data and meta_data["PatientID"]:

            elif meta_data.get("PatientID"):

                patient_directory = meta_data["PatientID"][0]

            elif "StudyInstanceUID" in meta_data and meta_data["StudyInstanceUID"]:

            elif meta_data.get("StudyInstanceUID"):

                patient_directory = meta_data["StudyInstanceUID"][0]

            else:

                raise Exception("Cannot determine patient directory")

            # Study directory: <StudyID>_<StudyDescription>, both parts are

            # optional. If both tags are missing or empty, raise an exception

            study_directory = []

            if "StudyID" in meta_data and meta_data["StudyID"]:

            if meta_data.get("StudyID"):

                study_directory.append(

                    numpy.ravel([x for x in meta_data["StudyID"] if x])[0])

            if "StudyDescription" in meta_data and meta_data["StudyDescription"]:

            if meta_data.get("StudyDescription"):

                study_directory.append(

                    numpy.ravel([x for x in meta_data["StudyDescription"] if x])[0])

            if not study_directory:

                if "StudyInstanceUID" in meta_data and meta_data["StudyInstanceUID"]:

                if meta_data.get("StudyInstanceUID"):

                    study_directory = [meta_data["StudyInstanceUID"][0]]

                else:

                    raise Exception("Cannot determine study directory")

    @@ -177,18 +175,18 @@ def get_first_item(item):
  
            # Study directory: <SeriesNumber>_<SeriesDescription>, both parts are

            # optional. If both tags are missing or empty, raise an exception

            series_directory = []

            if "SeriesNumber" in meta_data and meta_data["SeriesNumber"]:

            if meta_data.get("SeriesNumber"):

                series_directory.append(str(get_series_number(meta_data)))

            if "SeriesDescription" in meta_data and meta_data["SeriesDescription"]:

            if meta_data.get("SeriesDescription"):

                series_directory.append(

                    numpy.ravel(

                        [x for x in meta_data["SeriesDescription"] if x])[0])

            elif "ProtocolName" in meta_data and meta_data["ProtocolName"]:

            elif meta_data.get("ProtocolName"):

                series_directory.append(

                    numpy.ravel([x for x in meta_data["ProtocolName"] if x])[0])

            if not series_directory:

                if "SeriesInstanceUID" in meta_data and meta_data["SeriesInstanceUID"]:

                if meta_data.get("SeriesInstanceUID"):

                    series_directory = [meta_data["SeriesInstanceUID"][0]]

                else:

                    raise Exception("Cannot determine series directory")

src/python/dicomifier/dicom_to_nifti/meta_data.py

-Original file line number
+Diff line change
@@ Expand Up / @@ -84,7 +84,7 @@ def get_meta_data(stack, cache=None): @@
         for i, (data_set, frame) in enumerate(stack):
             try:
                 sop_instance_uid = data_set[odil.registry.SOPInstanceUID][0]
-            except Exception as e:
+            except Exception:
                 raise
             # Fetch non-frame-specific elements from cache
             for tag, element in cache[sop_instance_uid].items():
@@ Expand Down Expand Up / @@ -170,7 +170,7 @@ def get_tag_name(tag): @@
         try:
             tag_name = tag.get_name()
-        except odil.Exception as e:
+        except odil.Exception:
             tag_name = str(tag)
         return tag_name
@@ Expand All / @@ -182,9 +182,7 @@ def convert_element(element, specific_character_set): @@
         result = None
         # element can be None because a get is called above
-        if element is None:
-            result = None
-        elif element.empty():
+        if element is None or element.empty():
             result = None
         elif element.is_int() or element.is_real():
             result = list(element)
@@ Expand Down @@

src/python/dicomifier/dicom_to_nifti/series/__init__.py

            
                      Original file line number
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    @@ -21,8 +21,8 @@ def split_series(files):
  
        """

        logger.info(

            "Splitting %d DICOM file%s in series",

                len(files), "s" if len(files) > 1 else "")

            "Splitting {} DICOM file{} in series".format(

                len(files), "s" if len(files) > 1 else ""))

        series = {}

        for file_ in files:

    @@ -31,7 +31,7 @@ def split_series(files):
  
                    file_,  

                    halt_condition=lambda x: x>odil.registry.SeriesInstanceUID)

            except odil.Exception as e:

                logger.warning("Could not read %s: %s" % (file_, e))

                logger.warning(f"Could not read {file_}: {e}")

                continue

            uncompressed_ts = [

    @@ -43,7 +43,7 @@ def split_series(files):
  
                ]]

            if header[odil.registry.TransferSyntaxUID][0] not in uncompressed_ts:

                logger.warning(

                    "Could not read %s: compressed transfer syntax", file_)

                    f"Could not read {file_}: compressed transfer syntax")

                continue

            series_instance_uid = None

    @@ -55,13 +55,13 @@ def split_series(files):
  
                    series_instance_uid = finder(data_set)

                except Exception as e:

                    logger.warning(

                        "Could not run %s: %s" % (finder_class.__name__, e))

                        f"Could not run {finder_class.__name__}: {e}")

                    continue

                if series_instance_uid is not None:

                    break

            if series_instance_uid is None:

                logger.warning("Could not find a series for %s", file_)

                logger.warning(f"Could not find a series for {file_}")

                continue

            series.setdefault(finder, []).append(file_)

src/python/dicomifier/dicom_to_nifti/siemens.py

            
                      Original file line number
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    @@ -48,7 +48,7 @@ def parse_value(value, name):
  
            if value.startswith(b"0x"):

                return int(value.split()[0], 16)

            elif value.startswith(b"\""):

            elif value.startswith(b'"'):

                return re.findall(br'""(.*)""', value)[0].decode()

            else:

                int_match = re.match(br"^[+-]?\d+$", value)

    @@ -138,9 +138,9 @@ def parse_item(csa, start):
  
        length = struct.unpack(format, csa[start:start+header_size])

        format = ("<"    # Little endian

                  "{0}s" # Content

                  "{1}s" # Padding (?)

                 ).format(length[1], (4-length[1]%4)%4)

                  f"{length[1]}s" # Content

                  f"{(4-length[1]%4)%4}s" # Padding (?)

                 )

        content_size = struct.calcsize(format)

        content, padding = struct.unpack(

            format, csa[start+header_size:start+header_size+content_size])

    @@ -206,7 +206,7 @@ def value_parser(type_, value):
  
                    element)

                is_array, type_, name, index = match.groups()

                full_name = "{}{}{}".format(is_array.decode(), type_.decode(), name.decode())

                full_name = f"{is_array.decode()}{type_.decode()}{name.decode()}"

                is_array = (is_array == b"a")

                if index:

src/python/dicomifier/dicom_to_nifti/stacks.py

            
                      Original file line number
                      Diff line number
                      Diff line change
                  
    @@ -91,10 +91,10 @@ def build_selector(
  
        # Normalize the keys so that all stacks have the same key fields

        key_items = set()

        for key in stacks.keys():

        for key in stacks:

            key_items.update(x[0] for x in key)

        normalized_keys = {}

        for key in stacks.keys():

        for key in stacks:

            normalized_keys[key] = list(key)

            for key_item in key_items:

                if key_item not in [x[0] for x in key]:

    @@ -559,7 +559,7 @@ def _find_private_creator(data_set, private_creator, group):
  
        tag = odil.Tag(group, 0x0000)

        private_group = None

        for element in range(0, 256):

        for element in range(256):

            tag.element = element

            # Get the content of the potential private creator. It may be stored as

tests/diff/to_dicom.py

            
                      Original file line number
                      Diff line number
                      Diff line change
                  
    @@ -45,7 +45,7 @@ def main():
  
                            "to-dicom", "--dicomdir"]

                        +arguments

                        +[case_input, case_output])

                except subprocess.CalledProcessError as e:

                except subprocess.CalledProcessError:

                    return 1

                different |= diff_directories(case_baseline, case_output)

    @@ -92,8 +92,8 @@ def diff_directories(baseline, test):
  
            for filename in filenames:

                if not os.path.isfile(os.path.join(baseline_pathname, filename)):

                    different = True

                    print("{} missing in baseline".format(

                        os.path.join(relative_pathname, filename)))

                    relative_filename = os.path.join(relative_pathname, filename)

                    print(f"{relative_filename} missing in baseline")

        return different

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