From 1082e476f9f00bd4e45df2f9262b344718a83ee6 Mon Sep 17 00:00:00 2001 From: Jermiah Joseph Date: Mon, 5 Feb 2024 22:39:23 -0500 Subject: [PATCH 1/8] fix: Fix encryption key in OAuth2 class --- src/nbiatoolkit/auth.py | 6 +----- 1 file changed, 1 insertion(+), 5 deletions(-) diff --git a/src/nbiatoolkit/auth.py b/src/nbiatoolkit/auth.py index feb04cb..31da6a0 100644 --- a/src/nbiatoolkit/auth.py +++ b/src/nbiatoolkit/auth.py @@ -111,7 +111,7 @@ def __init__( self._fernet_key: bytes = Fernet.generate_key() self.username: str self.password: str - self.username, self.password = encrypt_credentials(key=self.fernet_key, username=username, password=password) + self.username, self.password = encrypt_credentials(key=self._fernet_key, username=username, password=password) if isinstance(base_url, NBIA_ENDPOINTS): self.base_url = base_url.value @@ -125,10 +125,6 @@ def __init__( self.scope = None - @property - def fernet_key(self) -> bytes: - return self._fernet_key - def is_logged_out(self) -> bool: return (self._access_token is "" and self.username == "" and self.password == "" and self.client_id == "" and self.base_url == "") From 18b6625df5a1d435aaad37d4d920b5198e0e58d3 Mon Sep 17 00:00:00 2001 From: Jermiah Joseph Date: Mon, 5 Feb 2024 22:39:42 -0500 Subject: [PATCH 2/8] feat: Add getDICOMTags method to NBIAClient class --- src/nbiatoolkit/dicomsort/dcm_qt_tree.py | 108 ++++++++++++++ src/nbiatoolkit/dicomsort/test_dicom_class.py | 139 ++++++++++++++++++ src/nbiatoolkit/dicomsort/test_tree.py | 132 +++++++++++++++++ src/nbiatoolkit/nbia.py | 18 +++ src/nbiatoolkit/utils/nbia_endpoints.py | 2 +- tests/test_nbia.py | 42 +++++- 6 files changed, 439 insertions(+), 2 deletions(-) create mode 100644 src/nbiatoolkit/dicomsort/dcm_qt_tree.py create mode 100644 src/nbiatoolkit/dicomsort/test_dicom_class.py create mode 100644 src/nbiatoolkit/dicomsort/test_tree.py diff --git a/src/nbiatoolkit/dicomsort/dcm_qt_tree.py b/src/nbiatoolkit/dicomsort/dcm_qt_tree.py new file mode 100644 index 0000000..1aa9226 --- /dev/null +++ b/src/nbiatoolkit/dicomsort/dcm_qt_tree.py @@ -0,0 +1,108 @@ +# dcm_qt_tree.py +"""View DICOM files in a tree using Qt and PySide2""" +# Copyright (c) 2013 Padraig Looney +# This file is released under the +# pydicom (https://github.com/pydicom/pydicom) +# license, see the file LICENSE available at +# (https://github.com/pydicom/pydicom) + +import pydicom +import sys +from PySide2 import QtGui +import collections + + +# # dcm_qt_tree.py +# """View DICOM files in a tree using Qt and PySide""" +# # Copyright (c) 2013 Padraig Looney +# # This file is released under the +# # pydicom (https://github.com/pydicom/pydicom) +# # license, see the file LICENSE available at +# # (https://github.com/pydicom/pydicom) + +# import pydicom +# import sys +# from PySide import QtGui +# import collections + + +# class DicomTree(object): +# def __init__(self, filename): +# self.filename = filename +# def show_tree(self): +# ds = self.dicom_to_dataset(self.filename) +# dic = self.dataset_to_dic(ds) +# model = self.dic_to_model(dic) +# self.display(model) +# def array_to_model(self, array): +# model = QtGui.QStandardItemModel() +# parentItem = model.invisibleRootItem() +# for ntuple in array: +# tag = ntuple[0] +# value = ntuple[1] +# if isinstance(value, dict): +# self.recurse_dic_to_item(value, parentItem) +# else: +# item = QtGui.QStandardItem(tag + str(value)) +# parentItem.appendRow(item) +# return parentItem +# def dic_to_model(self, dic): +# model = QtGui.QStandardItemModel() +# parentItem = model.invisibleRootItem() +# self.recurse_dic_to_item(dic, parentItem) +# return model +# def dataset_to_array(self, dataset): +# array = [] +# for data_element in dataset: +# array.append(self.data_element_to_dic(data_element)) +# return array +# def recurse_dic_to_item(self, dic, parent): +# for k in dic: +# v = dic[k] +# if isinstance(v, dict): +# item = QtGui.QStandardItem(k + ':' + str(v)) +# parent.appendRow(self.recurse_dic_to_item(v, item)) +# else: +# item = QtGui.QStandardItem(k + ': ' + str(v)) +# parent.appendRow(item) +# return parent +# def dicom_to_dataset(self, filename): +# dataset = pydicom.dcmread(filename, force=True) +# return dataset +# def data_element_to_dic(self, data_element): +# dic = collections.OrderedDict() +# if data_element.VR == "SQ": +# items = collections.OrderedDict() +# dic[data_element.name] = items +# i = 0 +# for dataset_item in data_element: +# items['item ' + str(i)] = self.dataset_to_dic(dataset_item) +# i += 1 +# elif data_element.name != 'Pixel Data': +# dic[data_element.name] = data_element.value +# return dic +# def dataset_to_dic(self, dataset): +# dic = collections.OrderedDict() +# for data_element in dataset: +# dic.update(self.data_element_to_dic(data_element)) +# return dic +# def display(self, model): +# app = QtGui.QApplication.instance() +# # create QApplication if it doesnt exist +# if not app: +# app = QtGui.QApplication(sys.argv) +# tree = QtGui.QTreeView() +# tree.setModel(model) +# tree.show() +# app.exec_() +# return tree + + +# def main(): +# filename = sys.argv[1] +# dicomTree = DicomTree(filename) +# dicomTree.show_tree() + + +# if __name__ == "__main__": +# main() diff --git a/src/nbiatoolkit/dicomsort/test_dicom_class.py b/src/nbiatoolkit/dicomsort/test_dicom_class.py new file mode 100644 index 0000000..7dfca75 --- /dev/null +++ b/src/nbiatoolkit/dicomsort/test_dicom_class.py @@ -0,0 +1,139 @@ + + +import pydicom +from dataclasses import dataclass +from typing import Optional + +@dataclass +class DicomData: + study_instance_uid: Optional[str] = None + series_instance_uid: Optional[str] = None + sop_instance_uid: Optional[str] = None + image_type: Optional[str] = None + study_id: Optional[str] = None + series_number: Optional[int] = None + acquisition_number: Optional[int] = None + instance_number: Optional[int] = None + image_position_patient: Optional[str] = None + image_orientation_patient: Optional[str] = None + frame_of_reference_uid: Optional[str] = None + position_reference_indicator: Optional[str] = None + slice_location: Optional[str] = None + samples_per_pixel: Optional[int] = None + rows: Optional[int] = None + columns: Optional[int] = None + pixel_spacing: Optional[str] = None + study_date: Optional[str] = None + series_date: Optional[str] = None + modality: Optional[str] = None + study_description: Optional[str] = None + series_description: Optional[str] = None + patient_name: Optional[str] = None + patient_id: Optional[str] = None + patient_birth_date: Optional[str] = None + patient_sex: Optional[str] = None + patient_age: Optional[str] = None + instance_creation_date: Optional[str] = None + instance_creation_time: Optional[str] = None + + def to_dataset(self): + ds = pydicom.Dataset() + ds.StudyInstanceUID = self.study_instance_uid + ds.SeriesInstanceUID = self.series_instance_uid + ds.SOPInstanceUID = self.sop_instance_uid + ds.ImageType = self.image_type + ds.StudyID = self.study_id + ds.SeriesNumber = self.series_number + ds.AcquisitionNumber = self.acquisition_number + ds.InstanceNumber = self.instance_number + ds.ImagePositionPatient = self.image_position_patient + ds.ImageOrientationPatient = self.image_orientation_patient + ds.FrameOfReferenceUID = self.frame_of_reference_uid + ds.PositionReferenceIndicator = self.position_reference_indicator + ds.SliceLocation = self.slice_location + ds.SamplesPerPixel = self.samples_per_pixel + ds.Rows = self.rows + ds.Columns = self.columns + ds.PixelSpacing = self.pixel_spacing + ds.StudyDate = self.study_date + ds.SeriesDate = self.series_date + ds.Modality = self.modality + ds.StudyDescription = self.study_description + ds.SeriesDescription = self.series_description + ds.PatientName = self.patient_name + ds.PatientID = self.patient_id + ds.PatientBirthDate = self.patient_birth_date + ds.PatientSex = self.patient_sex + ds.PatientAge = self.patient_age + ds.InstanceCreationDate = self.instance_creation_date + ds.InstanceCreationTime = self.instance_creation_time + + return ds + +def read_subset_dicom(file_path): + ds = pydicom.dcmread(file_path) + dicom_data = DicomData( + study_instance_uid=ds.get("StudyInstanceUID"), + series_instance_uid=ds.get("SeriesInstanceUID"), + sop_instance_uid=ds.get("SOPInstanceUID"), + image_type=ds.get("ImageType"), + study_id=ds.get("StudyID"), + series_number=ds.get("SeriesNumber"), + acquisition_number=ds.get("AcquisitionNumber"), + instance_number=ds.get("InstanceNumber"), + image_position_patient=ds.get("ImagePositionPatient"), + image_orientation_patient=ds.get("ImageOrientationPatient"), + frame_of_reference_uid=ds.get("FrameOfReferenceUID"), + position_reference_indicator=ds.get("PositionReferenceIndicator"), + slice_location=ds.get("SliceLocation"), + samples_per_pixel=ds.get("SamplesPerPixel"), + rows=ds.get("Rows"), + columns=ds.get("Columns"), + pixel_spacing=ds.get("PixelSpacing"), + study_date=ds.get("StudyDate"), + series_date=ds.get("SeriesDate"), + modality=ds.get("Modality"), + study_description=ds.get("StudyDescription"), + series_description=ds.get("SeriesDescription"), + patient_name=ds.get("PatientName"), + patient_id=ds.get("PatientID"), + patient_birth_date=ds.get("PatientBirthDate"), + patient_sex=ds.get("PatientSex"), + patient_age=ds.get("PatientAge"), + instance_creation_date=ds.get("InstanceCreationDate"), + instance_creation_time=ds.get("InstanceCreationTime") + ) + return dicom_data + + +def create_DicomData_from_DICT(data_list): + dicom_data = DicomData( + study_instance_uid=data_list.get("StudyInstanceUID"), + series_instance_uid=data_list.get("SeriesInstanceUID"), + sop_instance_uid=data_list.get("SOPInstance"), + image_type=data_list.get("ImageType"), + study_id=data_list.get("StudyID"), + series_number=data_list.get("SeriesNumber"), + acquisition_number=data_list.get("AcquisitionNumber"), + instance_number=data_list.get("InstanceNumber"), + image_position_patient=data_list.get("ImagePositionPatient"), + image_orientation_patient=data_list.get("ImageOrientationPatient"), + frame_of_reference_uid=data_list.get("FrameOfReferenceUID"), + position_reference_indicator=data_list.get("PositionReferenceIndicator"), + slice_location=data_list.get("SliceLocation"), + samples_per_pixel=data_list.get("SamplesPerPixel"), + rows=data_list.get("Rows"), + columns=data_list.get("Columns"), + pixel_spacing=data_list.get("PixelSpacing"), + study_date=data_list.get("StudyDate"), + series_date=data_list.get("SeriesDate"), + modality=data_list.get("Modality"), + study_description=data_list.get("StudyDescription"), + series_description=data_list.get("SeriesDescription"), + patient_name=data_list.get("PatientName"), + patient_id=data_list.get("PatientID"), + patient_birth_date=data_list.get("PatientBirthDate"), + patient_age=data_list.get("PatientAge"), + instance_creation_date=data_list.get("InstanceCreationDate"), + instance_creation_time=data_list.get("InstanceCreationTime") + ) \ No newline at end of file diff --git a/src/nbiatoolkit/dicomsort/test_tree.py b/src/nbiatoolkit/dicomsort/test_tree.py new file mode 100644 index 0000000..36334f6 --- /dev/null +++ b/src/nbiatoolkit/dicomsort/test_tree.py @@ -0,0 +1,132 @@ + +import sys + +import pydicom +from PyQt5.QtCore import Qt +from PyQt5.QtGui import QStandardItem, QStandardItemModel +from PyQt5.QtWidgets import (QApplication, QDesktopWidget, QTreeView, + QVBoxLayout, QWidget) + + +class DicomTree(QWidget): + def __init__(self, filename): + super().__init__() + self.filename = filename + self.setWindowTitle('DICOM Tree') + self.setGeometry(0, 0, 800, 600) + self.center() + + self.create_model() + self.init_tree() + self.show() + + def center(self): + # Get geometry of the main window + qr = self.frameGeometry() + # Get the center point of screen + cp = QDesktopWidget().availableGeometry().center() + # Move rectangle's center point to screen's center point + qr.moveCenter(cp) + # top left of rectangle becomes top left of window centering it + self.move(qr.topLeft()) + + def create_model(self): + model = QStandardItemModel(0, 5, self) + model.setHeaderData(0, Qt.Horizontal, "Name") + model.setHeaderData(1, Qt.Horizontal, "Value") + model.setHeaderData(2, Qt.Horizontal, "Tag") + model.setHeaderData(3, Qt.Horizontal, "VM") + model.setHeaderData(4, Qt.Horizontal, "VR") + parentItem = model.invisibleRootItem() + + ds = pydicom.read_file(self.filename, force=True) + self.recurse_dicom_tree(ds, parentItem) + self.model = model + + def init_tree(self): + self.tree = QTreeView() + self.tree.setModel(self.model) + mainLayout = QVBoxLayout() + mainLayout.addWidget(self.tree) + self.setLayout(mainLayout) + self.tree.setAlternatingRowColors(True) + [self.tree.resizeColumnToContents(x) for x in range(5)] + + def recurse_dicom_tree(self, ds, parent, name=None): + for _, data_element in enumerate(ds): + # If this is non-sequence element, add directly to parent + # print('aa', data_element, 'bb') + if not (data_element.VR == 'SQ'): + self.add_item_to_tree(data_element, parent) + else: + # Create the parent sequence in tree + seq_parent = self.add_item_to_tree(data_element, parent) + # For each item in sequence create a child + for i, seq_ds in enumerate(data_element.value): + # break + seq_item_description = data_element.name.replace( + " Sequence", "") + name = "%s %d" % (seq_item_description, i+1) + seq_item = self.add_item_to_tree(seq_ds, seq_parent, name) + # Append the contents of each sequence item as a grandchild + self.recurse_dicom_tree(seq_ds, seq_item, name) + return parent + + def add_item_to_tree(self, data_element, parent, element_name=None): + if element_name: + cols = [element_name, '', '', '', ''] + else: + value = '' if data_element.VR == 'SQ' else data_element.value + if (data_element.name == 'Pixel Data'): + value = 'Array of ' + str(len(data_element.value)) + ' bytes' + cols = [data_element.name, str(value), str(data_element.tag), str( + data_element.VM), str(data_element.VR)] + parent.appendRow([QStandardItem(c) for c in cols]) + last_parent = parent.child(parent.rowCount()-1) + + return last_parent + + +def main(): + app = QApplication(sys.argv) + filename = sys.argv[1] + dicomtree = DicomTree(filename) + sys.exit(app.exec_()) + + +if __name__ == "__main__": + main() +# s to command line arguments +# import sys + + +# class DicomTree(object): + +# def __init__(self, filename): +# self.filename = filename + +# def show_tree(self): +# ds = self.dicom_to_dataset(self.filename) +# dic = self.dataset_to_dic(ds) +# # model = self.dic_to_model(dic) +# # self.display(model) + +# def dicom_to_dataset(self, filename): +# dataset = pydicom.dcmread(filename, force=True, stop_before_pixels=True) +# return dataset + +# def dataset_to_dic(self, dataset): +# dic = collections.OrderedDict() +# for data_element in dataset: +# dic[data_element.name] = data_element.value +# return dic + +# if __name__ == '__main__': +# path1 = "/Users/bhklab/Documents/GitHub/NBIA-toolkit/sandbox/P_00038_LEFT_CC.dcm/96009/63992/91294.dcm" +# # dt = DicomTree(path1) +# app = QApplication(sys.argv) + +# window = QPushButton("Push Me") +# window.show() + +# app.exec_() \ No newline at end of file diff --git a/src/nbiatoolkit/nbia.py b/src/nbiatoolkit/nbia.py index fb78217..7d9367e 100644 --- a/src/nbiatoolkit/nbia.py +++ b/src/nbiatoolkit/nbia.py @@ -383,6 +383,24 @@ def getNewSeries( return response + def getDICOMTags( + self, + SeriesInstanceUID: str, + ) -> Union[list[dict], None]: + assert SeriesInstanceUID is not None and isinstance(SeriesInstanceUID, str), \ + "SeriesInstanceUID must be a string" + + PARAMS = self.parsePARAMS({"SeriesUID": SeriesInstanceUID}) + + response = self.query_api(endpoint=NBIA_ENDPOINTS.GET_DICOM_TAGS, params=PARAMS) + + if not isinstance(response, list): + self._log.error("Expected list, but received: %s", type(response)) + return None + + return response + + def downloadSeries( self, SeriesInstanceUID: Union[str, list], diff --git a/src/nbiatoolkit/utils/nbia_endpoints.py b/src/nbiatoolkit/utils/nbia_endpoints.py index 8f7574e..8c6e438 100644 --- a/src/nbiatoolkit/utils/nbia_endpoints.py +++ b/src/nbiatoolkit/utils/nbia_endpoints.py @@ -27,7 +27,7 @@ class NBIA_ENDPOINTS(Enum): GET_UPDATED_SERIES = "v2/getUpdatedSeries" # ?fromDate=01/01/2024 GET_SERIES_METADATA = "v1/getSeriesMetaData" DOWNLOAD_SERIES = "v2/getImageWithMD5Hash" - + GET_DICOM_TAGS = "getDicomTags" diff --git a/tests/test_nbia.py b/tests/test_nbia.py index 42f78b7..8df3e1d 100644 --- a/tests/test_nbia.py +++ b/tests/test_nbia.py @@ -4,6 +4,7 @@ # To run only one of the tests: # pytest -v -n 8 tests/test_nbia.py::test_getCollections +import imp import pytest from src.nbiatoolkit import NBIAClient from tempfile import TemporaryDirectory @@ -252,4 +253,43 @@ def test_nbiaclient_exit(nbia_client): with nbia_client: collections = nbia_client.getCollections() assert not nbia_client._oauth2_client.is_logged_out() - assert nbia_client._oauth2_client.is_logged_out() # Assuming there is a method to check if the client is logged out \ No newline at end of file + assert nbia_client._oauth2_client.is_logged_out() # Assuming there is a method to check if the client is logged out + + +def test_getDICOMTags(nbia_client: NBIAClient): + seriesUID = "1.3.6.1.4.1.14519.5.2.1.6834.5010.322628904903035357840500590726" + tags = nbia_client.getDICOMTags(seriesUID) + importantTags = [ + "Study Instance UID", + "Series Instance UID", + "SOP Instance UID", + "Image Type", + "Study ID", + "Series Number", + "Acquisition Number", + "Instance Number", + "Image Position (Patient)", + "Image Orientation (Patient)", + "Frame of Reference UID", + "Position Reference Indicator", + "Slice Location", + "Samples per Pixel", + "Rows", + "Columns", + "Pixel Spacing", + "Study Date", + "Series Date", + "Modality", + "Study Description", + "Series Description", + "Patient's Name", + "Patient ID", + "Patient's Birth Date", + "Patient's Sex", + "Patient's Age", + "Instance Creation Date", + "Instance Creation Time",] + print(seriesUID) + all_names = [tag["name"] for tag in tags] + for tag in importantTags: + assert tag in all_names From b78edd842f230b75d54e11d91a91c9979a2b8380 Mon Sep 17 00:00:00 2001 From: Jermiah Joseph Date: Sun, 11 Feb 2024 19:28:19 -0500 Subject: [PATCH 3/8] fix: Update pydicom version to 2.4.0 --- poetry.lock | 2 +- pyproject.toml | 2 +- src/nbiatoolkit/dicomsort/crawl.py | 229 ----------------------- src/nbiatoolkit/dicomsort/dcm_qt_tree.py | 108 ----------- 4 files changed, 2 insertions(+), 339 deletions(-) delete mode 100644 src/nbiatoolkit/dicomsort/crawl.py delete mode 100644 src/nbiatoolkit/dicomsort/dcm_qt_tree.py diff --git a/poetry.lock b/poetry.lock index e23a39b..fa186f9 100644 --- a/poetry.lock +++ b/poetry.lock @@ -3458,4 +3458,4 @@ testing = ["big-O", "jaraco.functools", "jaraco.itertools", "more-itertools", "p [metadata] lock-version = "2.0" python-versions = ">=3.10 || 3.12" -content-hash = "4157ce70160399191a3818d19cf069c6e13a4cf711e8159b96d81ca17c0a4579" +content-hash = "36633131d631259aff7c3add09927ad5f9363c22de0d1ab6b24286b2adb5563f" diff --git a/pyproject.toml b/pyproject.toml index 42f3335..214d57a 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -21,7 +21,7 @@ downloadSingleSeries = "nbiatoolkit.nbia_cli:downloadSingleSeries_cli" [tool.poetry.dependencies] python = ">=3.10 || 3.12" requests = "2.31.0" -pydicom = "^2.4.3" +pydicom = "^2.4.0" tqdm = "^4.66.1" pyfiglet = "^1.0" beautifulsoup4 = "^4.12.3" diff --git a/src/nbiatoolkit/dicomsort/crawl.py b/src/nbiatoolkit/dicomsort/crawl.py deleted file mode 100644 index 62eba30..0000000 --- a/src/nbiatoolkit/dicomsort/crawl.py +++ /dev/null @@ -1,229 +0,0 @@ -from argparse import ArgumentParser -import os -import pathlib -import glob -import json -import pandas as pd -from pydicom import dcmread -from tqdm import tqdm -from joblib import Parallel, delayed - - -def crawl_one(folder): - folder_path = pathlib.Path(folder) - database = {} - for path, _, _ in os.walk(folder): - # find dicoms - dicoms = glob.glob(pathlib.Path(path, "**", "*.dcm").as_posix(), recursive=True) - # print('\n', folder, dicoms) - # instance (slice) information - for dcm in dicoms: - try: - dcm_path = pathlib.Path(dcm) - # parent = dcm_path.parent#.as_posix() - fname = dcm_path.name - rel_path = dcm_path.relative_to(folder_path.parent.parent) # rel_path of dicom from folder - rel_posix = rel_path.parent.as_posix() # folder name + until parent folder of dicom - - meta = dcmread(dcm, force=True, stop_before_pixels=True) - patient = str(meta.PatientID) - study = str(meta.StudyInstanceUID) - series = str(meta.SeriesInstanceUID) - instance = str(meta.SOPInstanceUID) - - reference_ct, reference_rs, reference_pl, = "", "", "" - tr, te, tesla, scan_seq, elem = "", "", "", "", "" - try: - orientation = str(meta.ImageOrientationPatient) # (0020, 0037) - except: - orientation = "" - - try: - orientation_type = str(meta.AnatomicalOrientationType) # (0010, 2210) - except: - orientation_type = "" - - try: # RTSTRUCT - reference_ct = str(meta.ReferencedFrameOfReferenceSequence[0].RTReferencedStudySequence[0].RTReferencedSeriesSequence[0].SeriesInstanceUID) - except: - try: # SEGMENTATION - reference_ct = str(meta.ReferencedSeriesSequence[0].SeriesInstanceUID) - except: - try: # RTDOSE - reference_rs = str(meta.ReferencedStructureSetSequence[0].ReferencedSOPInstanceUID) - except: - pass - try: - reference_ct = str(meta.ReferencedImageSequence[0].ReferencedSOPInstanceUID) - except: - pass - try: - reference_pl = str(meta.ReferencedRTPlanSequence[0].ReferencedSOPInstanceUID) - except: - pass - - # MRI Tags - try: - tr = float(meta.RepetitionTime) - except: - pass - try: - te = float(meta.EchoTime) - except: - pass - try: - scan_seq = str(meta.ScanningSequence) - except: - pass - try: - tesla = float(meta.MagneticFieldStrength) - except: - pass - try: - elem = str(meta.ImagedNucleus) - except: - pass - - # Frame of Reference UIDs - try: - reference_frame = str(meta.FrameOfReferenceUID) - except: - try: - reference_frame = str(meta.ReferencedFrameOfReferenceSequence[0].FrameOfReferenceUID) - except: - reference_frame = "" - - try: - study_description = str(meta.StudyDescription) - except: - study_description = "" - - try: - series_description = str(meta.SeriesDescription) - except: - series_description = "" - - try: - subseries = str(meta.AcquisitionNumber) - except: - subseries = "default" - - if patient not in database: - database[patient] = {} - if study not in database[patient]: - database[patient][study] = {'description': study_description} - if series not in database[patient][study]: - rel_crawl_path = rel_posix - if meta.Modality == 'RTSTRUCT': - rel_crawl_path = os.path.join(rel_crawl_path, fname) - - database[patient][study][series] = {'description': series_description} - if subseries not in database[patient][study][series]: - database[patient][study][series][subseries] = {'instances': {}, - 'instance_uid': instance, - 'modality': meta.Modality, - 'reference_ct': reference_ct, - 'reference_rs': reference_rs, - 'reference_pl': reference_pl, - 'reference_frame': reference_frame, - 'folder': rel_crawl_path, - 'orientation': orientation, - 'orientation_type': orientation_type, - 'repetition_time':tr, - 'echo_time':te, - 'scan_sequence': scan_seq, - 'mag_field_strength': tesla, - 'imaged_nucleus': elem, - 'fname': rel_path.as_posix() # temporary until we switch to json-based loading - } - database[patient][study][series][subseries]['instances'][instance] = rel_path.as_posix() - except Exception as e: - print(folder, e) - pass - - return database - - -def to_df(database_dict): - df = pd.DataFrame() - for pat in database_dict: - for study in database_dict[pat]: - for series in database_dict[pat][study]: - if series != 'description': # skip description key in dict - for subseries in database_dict[pat][study][series]: - if subseries != 'description': # skip description key in dict - columns = ['patient_ID', 'study', 'study_description', - 'series', 'series_description', 'subseries', 'modality', - 'instances', 'instance_uid', - 'reference_ct', 'reference_rs', 'reference_pl', 'reference_frame', 'folder', - 'orientation', 'orientation_type', 'MR_repetition_time', 'MR_echo_time', - 'MR_scan_sequence', 'MR_magnetic_field_strength', 'MR_imaged_nucleus', 'file_path'] - values = [pat, study, database_dict[pat][study]['description'], - series, database_dict[pat][study][series]['description'], - subseries, database_dict[pat][study][series][subseries]['modality'], - len(database_dict[pat][study][series][subseries]['instances']), database_dict[pat][study][series][subseries]['instance_uid'], - database_dict[pat][study][series][subseries]['reference_ct'], database_dict[pat][study][series][subseries]['reference_rs'], - database_dict[pat][study][series][subseries]['reference_pl'], database_dict[pat][study][series][subseries]['reference_frame'], database_dict[pat][study][series][subseries]['folder'], - database_dict[pat][study][series][subseries]['orientation'], database_dict[pat][study][series][subseries]['orientation_type'], - database_dict[pat][study][series][subseries]['repetition_time'], database_dict[pat][study][series][subseries]['echo_time'], - database_dict[pat][study][series][subseries]['scan_sequence'], database_dict[pat][study][series][subseries]['mag_field_strength'], database_dict[pat][study][series][subseries]['imaged_nucleus'], - database_dict[pat][study][series][subseries]['fname'] - ] - - df_add = pd.DataFrame([values], columns=columns) - df = pd.concat([df, df_add], ignore_index=True) - return df - - -def crawl(top, - n_jobs: int = -1): - # top is the input directory in the argument parser from autotest.py - database_list = [] - folders = glob.glob(pathlib.Path(top, "*").as_posix()) - - database_list = Parallel(n_jobs=n_jobs)(delayed(crawl_one)(pathlib.Path(top, folder).as_posix()) for folder in tqdm(folders)) - - # convert list to dictionary - database_dict = {} - for db in database_list: - for key in db: - database_dict[key] = db[key] - - # save one level above imaging folders - parent, dataset = os.path.split(top) - - parent_imgtools = pathlib.Path(parent, ".imgtools").as_posix() - - if not os.path.exists(parent_imgtools): - try: - os.makedirs(parent_imgtools) - except: - pass - - # save as json - with open(pathlib.Path(parent_imgtools, f'imgtools_{dataset}.json').as_posix(), 'w') as f: - json.dump(database_dict, f, indent=4) - - # save as dataframe - df = to_df(database_dict) - df_path = pathlib.Path(parent_imgtools, f'imgtools_{dataset}.csv').as_posix() - df.to_csv(df_path) - - return database_dict - - -if __name__ == "__main__": - parser = ArgumentParser("Dataset DICOM Crawler") - parser.add_argument("directory", - type=str, - help="Top-level directory of the dataset.") - parser.add_argument("--n_jobs", - type=int, - default=16, - help="Number of parallel processes for multiprocessing.") - - args = parser.parse_args() - print(args.directory) - db = crawl(args.directory, n_jobs=args.n_jobs) - print(f"Length of database: {len(db)}") - diff --git a/src/nbiatoolkit/dicomsort/dcm_qt_tree.py b/src/nbiatoolkit/dicomsort/dcm_qt_tree.py deleted file mode 100644 index 1aa9226..0000000 --- a/src/nbiatoolkit/dicomsort/dcm_qt_tree.py +++ /dev/null @@ -1,108 +0,0 @@ -# dcm_qt_tree.py -"""View DICOM files in a tree using Qt and PySide2""" -# Copyright (c) 2013 Padraig Looney -# This file is released under the -# pydicom (https://github.com/pydicom/pydicom) -# license, see the file LICENSE available at -# (https://github.com/pydicom/pydicom) - -import pydicom -import sys -from PySide2 import QtGui -import collections - - -# # dcm_qt_tree.py -# """View DICOM files in a tree using Qt and PySide""" -# # Copyright (c) 2013 Padraig Looney -# # This file is released under the -# # pydicom (https://github.com/pydicom/pydicom) -# # license, see the file LICENSE available at -# # (https://github.com/pydicom/pydicom) - -# import pydicom -# import sys -# from PySide import QtGui -# import collections - - -# class DicomTree(object): -# def __init__(self, filename): -# self.filename = filename -# def show_tree(self): -# ds = self.dicom_to_dataset(self.filename) -# dic = self.dataset_to_dic(ds) -# model = self.dic_to_model(dic) -# self.display(model) -# def array_to_model(self, array): -# model = QtGui.QStandardItemModel() -# parentItem = model.invisibleRootItem() -# for ntuple in array: -# tag = ntuple[0] -# value = ntuple[1] -# if isinstance(value, dict): -# self.recurse_dic_to_item(value, parentItem) -# else: -# item = QtGui.QStandardItem(tag + str(value)) -# parentItem.appendRow(item) -# return parentItem -# def dic_to_model(self, dic): -# model = QtGui.QStandardItemModel() -# parentItem = model.invisibleRootItem() -# self.recurse_dic_to_item(dic, parentItem) -# return model -# def dataset_to_array(self, dataset): -# array = [] -# for data_element in dataset: -# array.append(self.data_element_to_dic(data_element)) -# return array -# def recurse_dic_to_item(self, dic, parent): -# for k in dic: -# v = dic[k] -# if isinstance(v, dict): -# item = QtGui.QStandardItem(k + ':' + str(v)) -# parent.appendRow(self.recurse_dic_to_item(v, item)) -# else: -# item = QtGui.QStandardItem(k + ': ' + str(v)) -# parent.appendRow(item) -# return parent -# def dicom_to_dataset(self, filename): -# dataset = pydicom.dcmread(filename, force=True) -# return dataset -# def data_element_to_dic(self, data_element): -# dic = collections.OrderedDict() -# if data_element.VR == "SQ": -# items = collections.OrderedDict() -# dic[data_element.name] = items -# i = 0 -# for dataset_item in data_element: -# items['item ' + str(i)] = self.dataset_to_dic(dataset_item) -# i += 1 -# elif data_element.name != 'Pixel Data': -# dic[data_element.name] = data_element.value -# return dic -# def dataset_to_dic(self, dataset): -# dic = collections.OrderedDict() -# for data_element in dataset: -# dic.update(self.data_element_to_dic(data_element)) -# return dic -# def display(self, model): -# app = QtGui.QApplication.instance() -# # create QApplication if it doesnt exist -# if not app: -# app = QtGui.QApplication(sys.argv) -# tree = QtGui.QTreeView() -# tree.setModel(model) -# tree.show() -# app.exec_() -# return tree - - -# def main(): -# filename = sys.argv[1] -# dicomTree = DicomTree(filename) -# dicomTree.show_tree() - - -# if __name__ == "__main__": -# main() From 91b277ba1a09f491bf8c8943dc4cf6f940f523d0 Mon Sep 17 00:00:00 2001 From: Jermiah Joseph Date: Sun, 11 Feb 2024 19:31:58 -0500 Subject: [PATCH 4/8] fix: remove extra files --- poetry.lock | 599 +++++++++--------- src/nbiatoolkit/dicomsort/test_dicom_class.py | 139 ---- src/nbiatoolkit/dicomsort/test_tree.py | 132 ---- 3 files changed, 303 insertions(+), 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deleted file mode 100644 index 7dfca75..0000000 --- a/src/nbiatoolkit/dicomsort/test_dicom_class.py +++ /dev/null @@ -1,139 +0,0 @@ - - -import pydicom -from dataclasses import dataclass -from typing import Optional - -@dataclass -class DicomData: - study_instance_uid: Optional[str] = None - series_instance_uid: Optional[str] = None - sop_instance_uid: Optional[str] = None - image_type: Optional[str] = None - study_id: Optional[str] = None - series_number: Optional[int] = None - acquisition_number: Optional[int] = None - instance_number: Optional[int] = None - image_position_patient: Optional[str] = None - image_orientation_patient: Optional[str] = None - frame_of_reference_uid: Optional[str] = None - position_reference_indicator: Optional[str] = None - slice_location: Optional[str] = None - samples_per_pixel: Optional[int] = None - rows: Optional[int] = None - columns: Optional[int] = None - pixel_spacing: Optional[str] = None - study_date: Optional[str] = None - series_date: Optional[str] = None - modality: Optional[str] = None - study_description: Optional[str] = None - series_description: Optional[str] = None - patient_name: Optional[str] = None - patient_id: Optional[str] = None - patient_birth_date: Optional[str] = None - patient_sex: Optional[str] = None - patient_age: Optional[str] = None - instance_creation_date: Optional[str] = None - instance_creation_time: Optional[str] = None - - def to_dataset(self): - ds = pydicom.Dataset() - ds.StudyInstanceUID = self.study_instance_uid - ds.SeriesInstanceUID = self.series_instance_uid - ds.SOPInstanceUID = self.sop_instance_uid - ds.ImageType = self.image_type - ds.StudyID = self.study_id - ds.SeriesNumber = self.series_number - ds.AcquisitionNumber = self.acquisition_number - ds.InstanceNumber = self.instance_number - ds.ImagePositionPatient = self.image_position_patient - ds.ImageOrientationPatient = self.image_orientation_patient - ds.FrameOfReferenceUID = self.frame_of_reference_uid - ds.PositionReferenceIndicator = self.position_reference_indicator - ds.SliceLocation = self.slice_location - ds.SamplesPerPixel = self.samples_per_pixel - ds.Rows = self.rows - ds.Columns = self.columns - ds.PixelSpacing = self.pixel_spacing - ds.StudyDate = self.study_date - ds.SeriesDate = self.series_date - ds.Modality = self.modality - ds.StudyDescription = self.study_description - ds.SeriesDescription = self.series_description - ds.PatientName = self.patient_name - ds.PatientID = self.patient_id - ds.PatientBirthDate = self.patient_birth_date - ds.PatientSex = self.patient_sex - ds.PatientAge = self.patient_age - ds.InstanceCreationDate = self.instance_creation_date - ds.InstanceCreationTime = self.instance_creation_time - - return ds - -def read_subset_dicom(file_path): - ds = pydicom.dcmread(file_path) - dicom_data = DicomData( - study_instance_uid=ds.get("StudyInstanceUID"), - series_instance_uid=ds.get("SeriesInstanceUID"), - sop_instance_uid=ds.get("SOPInstanceUID"), - image_type=ds.get("ImageType"), - study_id=ds.get("StudyID"), - series_number=ds.get("SeriesNumber"), - acquisition_number=ds.get("AcquisitionNumber"), - instance_number=ds.get("InstanceNumber"), - image_position_patient=ds.get("ImagePositionPatient"), - image_orientation_patient=ds.get("ImageOrientationPatient"), - frame_of_reference_uid=ds.get("FrameOfReferenceUID"), - position_reference_indicator=ds.get("PositionReferenceIndicator"), - slice_location=ds.get("SliceLocation"), - samples_per_pixel=ds.get("SamplesPerPixel"), - rows=ds.get("Rows"), - columns=ds.get("Columns"), - pixel_spacing=ds.get("PixelSpacing"), - study_date=ds.get("StudyDate"), - series_date=ds.get("SeriesDate"), - modality=ds.get("Modality"), - study_description=ds.get("StudyDescription"), - series_description=ds.get("SeriesDescription"), - patient_name=ds.get("PatientName"), - patient_id=ds.get("PatientID"), - patient_birth_date=ds.get("PatientBirthDate"), - patient_sex=ds.get("PatientSex"), - patient_age=ds.get("PatientAge"), - instance_creation_date=ds.get("InstanceCreationDate"), - instance_creation_time=ds.get("InstanceCreationTime") - ) - return dicom_data - - -def create_DicomData_from_DICT(data_list): - dicom_data = DicomData( - study_instance_uid=data_list.get("StudyInstanceUID"), - series_instance_uid=data_list.get("SeriesInstanceUID"), - sop_instance_uid=data_list.get("SOPInstance"), - image_type=data_list.get("ImageType"), - study_id=data_list.get("StudyID"), - series_number=data_list.get("SeriesNumber"), - acquisition_number=data_list.get("AcquisitionNumber"), - instance_number=data_list.get("InstanceNumber"), - image_position_patient=data_list.get("ImagePositionPatient"), - image_orientation_patient=data_list.get("ImageOrientationPatient"), - frame_of_reference_uid=data_list.get("FrameOfReferenceUID"), - position_reference_indicator=data_list.get("PositionReferenceIndicator"), - slice_location=data_list.get("SliceLocation"), - samples_per_pixel=data_list.get("SamplesPerPixel"), - rows=data_list.get("Rows"), - columns=data_list.get("Columns"), - pixel_spacing=data_list.get("PixelSpacing"), - study_date=data_list.get("StudyDate"), - series_date=data_list.get("SeriesDate"), - modality=data_list.get("Modality"), - study_description=data_list.get("StudyDescription"), - series_description=data_list.get("SeriesDescription"), - patient_name=data_list.get("PatientName"), - patient_id=data_list.get("PatientID"), - patient_birth_date=data_list.get("PatientBirthDate"), - patient_age=data_list.get("PatientAge"), - instance_creation_date=data_list.get("InstanceCreationDate"), - instance_creation_time=data_list.get("InstanceCreationTime") - ) \ No newline at end of file diff --git a/src/nbiatoolkit/dicomsort/test_tree.py b/src/nbiatoolkit/dicomsort/test_tree.py deleted file mode 100644 index 36334f6..0000000 --- a/src/nbiatoolkit/dicomsort/test_tree.py +++ /dev/null @@ -1,132 +0,0 @@ - -import sys - -import pydicom -from PyQt5.QtCore import Qt -from PyQt5.QtGui import QStandardItem, QStandardItemModel -from PyQt5.QtWidgets import (QApplication, QDesktopWidget, QTreeView, - QVBoxLayout, QWidget) - - -class DicomTree(QWidget): - def __init__(self, filename): - super().__init__() - self.filename = filename - self.setWindowTitle('DICOM Tree') - self.setGeometry(0, 0, 800, 600) - self.center() - - self.create_model() - self.init_tree() - self.show() - - def center(self): - # Get geometry of the main window - qr = self.frameGeometry() - # Get the center point of screen - cp = QDesktopWidget().availableGeometry().center() - # Move rectangle's center point to screen's center point - qr.moveCenter(cp) - # top left of rectangle becomes top left of window centering it - self.move(qr.topLeft()) - - def create_model(self): - model = QStandardItemModel(0, 5, self) - model.setHeaderData(0, Qt.Horizontal, "Name") - model.setHeaderData(1, Qt.Horizontal, "Value") - model.setHeaderData(2, Qt.Horizontal, "Tag") - model.setHeaderData(3, Qt.Horizontal, "VM") - model.setHeaderData(4, Qt.Horizontal, "VR") - parentItem = model.invisibleRootItem() - - ds = pydicom.read_file(self.filename, force=True) - self.recurse_dicom_tree(ds, parentItem) - self.model = model - - def init_tree(self): - self.tree = QTreeView() - self.tree.setModel(self.model) - mainLayout = QVBoxLayout() - mainLayout.addWidget(self.tree) - self.setLayout(mainLayout) - self.tree.setAlternatingRowColors(True) - [self.tree.resizeColumnToContents(x) for x in range(5)] - - def recurse_dicom_tree(self, ds, parent, name=None): - for _, data_element in enumerate(ds): - # If this is non-sequence element, add directly to parent - # print('aa', data_element, 'bb') - if not (data_element.VR == 'SQ'): - self.add_item_to_tree(data_element, parent) - else: - # Create the parent sequence in tree - seq_parent = self.add_item_to_tree(data_element, parent) - # For each item in sequence create a child - for i, seq_ds in enumerate(data_element.value): - # break - seq_item_description = data_element.name.replace( - " Sequence", "") - name = "%s %d" % (seq_item_description, i+1) - seq_item = self.add_item_to_tree(seq_ds, seq_parent, name) - # Append the contents of each sequence item as a grandchild - self.recurse_dicom_tree(seq_ds, seq_item, name) - return parent - - def add_item_to_tree(self, data_element, parent, element_name=None): - if element_name: - cols = [element_name, '', '', '', ''] - else: - value = '' if data_element.VR == 'SQ' else data_element.value - if (data_element.name == 'Pixel Data'): - value = 'Array of ' + str(len(data_element.value)) + ' bytes' - cols = [data_element.name, str(value), str(data_element.tag), str( - data_element.VM), str(data_element.VR)] - parent.appendRow([QStandardItem(c) for c in cols]) - last_parent = parent.child(parent.rowCount()-1) - - return last_parent - - -def main(): - app = QApplication(sys.argv) - filename = sys.argv[1] - dicomtree = DicomTree(filename) - sys.exit(app.exec_()) - - -if __name__ == "__main__": - main() -# s to command line arguments -# import sys - - -# class DicomTree(object): - -# def __init__(self, filename): -# self.filename = filename - -# def show_tree(self): -# ds = self.dicom_to_dataset(self.filename) -# dic = self.dataset_to_dic(ds) -# # model = self.dic_to_model(dic) -# # self.display(model) - -# def dicom_to_dataset(self, filename): -# dataset = pydicom.dcmread(filename, force=True, stop_before_pixels=True) -# return dataset - -# def dataset_to_dic(self, dataset): -# dic = collections.OrderedDict() -# for data_element in dataset: -# dic[data_element.name] = data_element.value -# return dic - -# if __name__ == '__main__': -# path1 = "/Users/bhklab/Documents/GitHub/NBIA-toolkit/sandbox/P_00038_LEFT_CC.dcm/96009/63992/91294.dcm" -# # dt = DicomTree(path1) -# app = QApplication(sys.argv) - -# window = QPushButton("Push Me") -# window.show() - -# app.exec_() \ No newline at end of file From 972c785b9ffef735ab9544819917d0a23b0d909f Mon Sep 17 00:00:00 2001 From: Jermiah Joseph Date: Sun, 11 Feb 2024 19:32:54 -0500 Subject: [PATCH 5/8] build: Add conditional upload of coverage report artifact --- .github/workflows/main.yml | 2 ++ 1 file changed, 2 insertions(+) diff --git a/.github/workflows/main.yml b/.github/workflows/main.yml index 45ca062..0e10226 100644 --- a/.github/workflows/main.yml +++ b/.github/workflows/main.yml @@ -36,6 +36,8 @@ jobs: poetry run pytest -n 4 --cov --cov-report xml:coverage-report/coverage.xml - name: Upload coverage report artifact to be used by Codecov + # only upload if matrix.os is ubuntu-latest and matrix.python-version is 3.12 + if: matrix.os == 'ubuntu-latest' && matrix.python-version == '3.12' uses: actions/upload-artifact@v2 with: name: coverage-report From 58a9ada2bdfc0ec126ff80ce3adff4608562001b Mon Sep 17 00:00:00 2001 From: Jermiah Joseph Date: Sun, 11 Feb 2024 19:34:07 -0500 Subject: [PATCH 6/8] fix: remove err --- tests/test_nbia.py | 1 - 1 file changed, 1 deletion(-) diff --git a/tests/test_nbia.py b/tests/test_nbia.py index 8df3e1d..6de122e 100644 --- a/tests/test_nbia.py +++ b/tests/test_nbia.py @@ -4,7 +4,6 @@ # To run only one of the tests: # pytest -v -n 8 tests/test_nbia.py::test_getCollections -import imp import pytest from src.nbiatoolkit import NBIAClient from tempfile import TemporaryDirectory From 8b67ab0a7b853e192c7112d7c3d6f6710153a510 Mon Sep 17 00:00:00 2001 From: github-actions Date: Mon, 12 Feb 2024 00:45:46 +0000 Subject: [PATCH 7/8] chore(sem-ver): 0.29.0 --- docs/markdowns/CHANGELOG.md | 65 +++++++++++++++++++++++++++++++++++++ pyproject.toml | 2 +- setup.py | 2 +- src/nbiatoolkit/nbia.py | 2 +- 4 files changed, 68 insertions(+), 3 deletions(-) diff --git a/docs/markdowns/CHANGELOG.md b/docs/markdowns/CHANGELOG.md index 9806487..bb83cd5 100644 --- a/docs/markdowns/CHANGELOG.md +++ b/docs/markdowns/CHANGELOG.md @@ -2,10 +2,75 @@ +## v0.29.0 (2024-02-12) + +### Build + +* build: Add conditional upload of coverage report artifact ([`972c785`](https://github.com/jjjermiah/nbia-toolkit/commit/972c785b9ffef735ab9544819917d0a23b0d909f)) + +### Chore + +* chore: Update README: 0.28.0 ([`92ff4eb`](https://github.com/jjjermiah/nbia-toolkit/commit/92ff4ebe8420bd3f63011424ec3bb44ebe286f4c)) + +### Feature + +* feat: Add getDICOMTags method to NBIAClient class ([`18b6625`](https://github.com/jjjermiah/nbia-toolkit/commit/18b6625df5a1d435aaad37d4d920b5198e0e58d3)) + +### Fix + +* fix: remove err ([`58a9ada`](https://github.com/jjjermiah/nbia-toolkit/commit/58a9ada2bdfc0ec126ff80ce3adff4608562001b)) + +* fix: remove extra files ([`91b277b`](https://github.com/jjjermiah/nbia-toolkit/commit/91b277ba1a09f491bf8c8943dc4cf6f940f523d0)) + +* fix: Update pydicom version to 2.4.0 ([`b78edd8`](https://github.com/jjjermiah/nbia-toolkit/commit/b78edd842f230b75d54e11d91a91c9979a2b8380)) + +* fix: merge ([`544c682`](https://github.com/jjjermiah/nbia-toolkit/commit/544c682d9300aae80def16a22e379602ef5a8370)) + +* fix: Fix encryption key in OAuth2 class ([`1082e47`](https://github.com/jjjermiah/nbia-toolkit/commit/1082e476f9f00bd4e45df2f9262b344718a83ee6)) + +### Refactor + +* refactor: clean, lint ([`688a1a6`](https://github.com/jjjermiah/nbia-toolkit/commit/688a1a6de485c14a9e20150fc1335635f3221f01)) + +### Unknown + +* Merge pull request #104 from jjjermiah/dicomtags + +feat: Dicomtags ([`25760ef`](https://github.com/jjjermiah/nbia-toolkit/commit/25760ef89c94dce23c4bf4ba8e5ba00fabe32c29)) + +* Merge pull request #103 from jjjermiah/devel + +refactor: clean, lint ([`f9ab11e`](https://github.com/jjjermiah/nbia-toolkit/commit/f9ab11e6980cd95b7b661465a0cc4796d8e8df66)) + +* remove unused lines ([`c1dc231`](https://github.com/jjjermiah/nbia-toolkit/commit/c1dc23113340d358cd201c36f2e1e9b1505644cc)) + +* Merge pull request #102 from jjjermiah/19-authpy-logout-functionality + +19 authpy logout functionality ([`fee4ee0`](https://github.com/jjjermiah/nbia-toolkit/commit/fee4ee0c870a178a459db9e15d8f521456daa170)) + +* tests: remove main code in md5 ([`2972b5f`](https://github.com/jjjermiah/nbia-toolkit/commit/2972b5fc9b7bb37dea525abeb9a1e8f1748bc072)) + +* tests: add more coverage for logger ([`b90c74c`](https://github.com/jjjermiah/nbia-toolkit/commit/b90c74c0bd7af5940e72401d17a5e41982466897)) + +* Merge pull request #101 from jjjermiah/19-authpy-logout-functionality + +19 authpy logout functionality ([`a6f40cc`](https://github.com/jjjermiah/nbia-toolkit/commit/a6f40cc506ce035e2a6568e1af546ded37b34677)) + +* tests: fix small error ([`977df6c`](https://github.com/jjjermiah/nbia-toolkit/commit/977df6c1ae29262f45963cb929d70fb446f5768a)) + +* Merge pull request #100 from jjjermiah/main + +merge ([`d2a6f55`](https://github.com/jjjermiah/nbia-toolkit/commit/d2a6f55cd6df0e98a122f8f94cb6512c8f3da65a)) + +* tests: add tests and Update user authentication logic ([`bf4b8d8`](https://github.com/jjjermiah/nbia-toolkit/commit/bf4b8d8737a5621c778c07c52d517a379741139a)) + + ## v0.28.0 (2024-02-05) ### Chore +* chore(sem-ver): 0.28.0 ([`4f78b7a`](https://github.com/jjjermiah/nbia-toolkit/commit/4f78b7a01e3d58d60ad83b039079198c0181324d)) + * chore: Update README: 0.27.0 ([`79f7eda`](https://github.com/jjjermiah/nbia-toolkit/commit/79f7edafff8bf0ada9f0ea14909c9fe45f628a69)) ### Feature diff --git a/pyproject.toml b/pyproject.toml index 214d57a..3cc2927 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -1,6 +1,6 @@ [tool.poetry] name = "nbiatoolkit" -version = "0.28.0" +version = "0.29.0" description = "A python package to query the National Biomedical Imaging Archive (NBIA) database." authors = ["Jermiah Joseph"] license = "MIT" diff --git a/setup.py b/setup.py index 5d039a7..fae74b0 100644 --- a/setup.py +++ b/setup.py @@ -1,6 +1,6 @@ from setuptools import setup -__version__ = "0.28.0" +__version__ = "0.29.0" setup( name="nbiatoolkit", diff --git a/src/nbiatoolkit/nbia.py b/src/nbiatoolkit/nbia.py index a5b9063..79dbbbd 100644 --- a/src/nbiatoolkit/nbia.py +++ b/src/nbiatoolkit/nbia.py @@ -20,7 +20,7 @@ from datetime import datetime # set __version__ variable -__version__ = "0.28.0" +__version__ = "0.29.0" class NBIAClient: From d10a38d401080863597e68818341fcdb0b77ba23 Mon Sep 17 00:00:00 2001 From: jjjermiah Date: Mon, 12 Feb 2024 00:48:18 +0000 Subject: [PATCH 8/8] chore: Update README: 0.29.0 --- README.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/README.md b/README.md index 3f6d190..02498b7 100644 --- a/README.md +++ b/README.md @@ -55,7 +55,7 @@ For quick access to the NBIA, the toolkit also provides a command line interface /_/ |_/_____/___/_/ |_/_/ \____/\____/_/_/|_/_/\__/ -Version: 0.28.0 +Version: 0.29.0 Available CLI tools: