When can I expect a new release?

I am looking for TM and DT VR's to be converted to date and timestamps. This was committed to the repo about 3 years ago but it is not in v0.9.9 for some reason?

There are over 640 commits between v0.9.9 and master. As a recommendation, I would definitely try to release more versions...

This pull request is intended to facilitate the creation of DICOM Structured Reports (SR).

It adds the sr package, which implements

• Template TID 1500 Measurement Report and other templates that may be included in the root template: pydicom.sr.templates
• Value Types of the SR Document Content Macro: pydicom.sr.value_types
• Context Groups (autogenerated from FHIR value set resources): pydicom.sr.context_groups

A few things still need to be completed. However, I was hoping to already get your feedback on the approach in general and whether you would be interested in including this code into the pydicom package.

I suggest @pieper, @fedorov, @seandoyle and @dclunie as reviewers. We had several discussions on how to implement SR at the 2019 NA-MIC project week and beyond.

Below is an example for creating a SR document using pydicom.sr (the resulting DICOM PS3.10 file is also included in the repository: pydicom/data/test_files/SR_comprehensive3d.dcm:

from pydicom.filereader import dcmread
from pydicom.uid import generate_uid
from pydicom.sr.context_groups.cid_4 import CERVICOTHORACIC_SPINE
from pydicom.sr.context_groups.cid_100 import CT_UNSPECIFIED_BODY_REGION
from pydicom.sr.context_groups.cid_218 import AREA_OF_DEFINED_REGION
from pydicom.sr.context_groups.cid_220 import NOT_SIGNIFICANT
from pydicom.sr.context_groups.cid_222 import NORMAL
from pydicom.sr.context_groups.cid_270 import PERSON, DEVICE
from pydicom.sr.context_groups.cid_6115 import VERTEBRAL_FORAMEN
from pydicom.sr.context_groups.cid_7151 import SPINAL_CORD
from pydicom.sr.context_groups.cid_7461 import SQUARE_CENTIMETER
from pydicom.sr.document import Comprehensive3DSR
from pydicom.sr.templates import (
    DeviceObserverIdentifyingAttributes,
    FindingSite,
    Measurement,
    MeasurementProperties,
    MeasurementReport,
    ObservationContext,
    ObserverContext,
    PersonObserverIdentifyingAttributes,
    PlanarROIMeasurementsAndQualitativeEvaluations,
    ReferencedRegion,
    ReferencedVolume,
    ROIMeasurements,
    SourceImageForRegion,
    SourceImageForSegmentation,
    SubjectContext,
    TrackingIdentifier,
    VolumetricROIMeasurementsAndQualitativeEvaluations,
)
from pydicom.sr.value_types import GraphicTypes

if __name__ == '__main__':

    ref_filename = 'pydicom/data/test_files/CT_small.dcm'
    ref_dataset = dcmread(ref_filename)

    observer_person_context = ObserverContext(
        observer_type=PERSON,
        observer_identifying_attributes=PersonObserverIdentifyingAttributes(
            name='Foo'
        )
    )
    observer_device_context = ObserverContext(
        observer_type=DEVICE,
        observer_identifying_attributes=DeviceObserverIdentifyingAttributes(
            uid=generate_uid()
        )
    )
    observation_context = ObservationContext(
        observer_person_context=observer_person_context,
        observer_device_context=observer_device_context,
    )

    region_reference = ReferencedRegion(
        graphic_type=GraphicTypes.CIRCLE,
        graphic_data=((58.0, 52.0), (58.0, 41.0)),
        source_image=SourceImageForRegion(
            sop_class_uid=ref_dataset.SOPClassUID,
            sop_instance_uid=ref_dataset.SOPInstanceUID
        )
    )
    finding_sites = [
        FindingSite(
            anatomic_location=CERVICOTHORACIC_SPINE,
            topographical_modifier=VERTEBRAL_FORAMEN
        ),
    ]
    measurements = [
        Measurement(
            name=AREA_OF_DEFINED_REGION,
            tracking_identifier=TrackingIdentifier(uid=generate_uid()),
            value=1.7,
            unit=SQUARE_CENTIMETER,
            properties=MeasurementProperties(
                normality=NORMAL,
                level_of_significance=NOT_SIGNIFICANT
            )
        )
    ]
    region_measurements = ROIMeasurements(
        measurements=measurements,
        finding_sites=finding_sites
    )
    imaging_measurements = PlanarROIMeasurementsAndQualitativeEvaluations(
        tracking_identifier=TrackingIdentifier(
            uid=generate_uid(),
            identifier='Planar ROI Measurements'
        ),
        referenced_region=region_reference,
        finding_type=SPINAL_CORD,
        measurements=region_measurements
    )
    measurement_report = MeasurementReport(
        observation_context=observation_context,
        procedure_reported=CT_UNSPECIFIED_BODY_REGION,
        imaging_measurements=imaging_measurements
    )

    document = Comprehensive3DSR(
        evidence=[ref_dataset],
        content=measurement_report,
        series_instance_uid=generate_uid(),
        series_number=1,
        series_description='Measurement Reports',
        sop_instance_uid=generate_uid(),
        instance_number=1,
        institution_name='Institution',
        institution_department_name='Institution Department',
        manufacturer='Manufacturer'
    )
    document_filename = '/tmp/{}.dcm'.format(document.SOPInstanceUID)
    document.save_as(document_filename)

Description

Hello, I am trying to use pydicom to open images in a dicom directory. But when I try to open an image, I have this error : NotImplementedError: No available image handler could decode this transfer syntax JPEG Lossless, Non-Hierarchical, First-Order Prediction (Process 14 [Selection Value 1])

Steps/Code to Reproduce

I run this :

for record in ds.DirectoryRecordSequence:
  if record.DirectoryRecordType == "IMAGE":
  # Extract the relative path to the DICOM file
        path = os.path.join(*record.ReferencedFileID)
        dcm = dicom.read_file(path)
        d = dcm.pixel_array

and it output the NotImplemented Error

Versions

I have tried with pydicom 1.0.

Do you have any idea how to solve this error or another package to open these images ?
Thank you very much in advance.

Reference Issue

This PR will fix #430 by adding a data_files specification in the setup.py

What does this implement/fix? Explain your changes.

We basically needed to define the variable data_files as a list of tuples, each with a relative path to a folder, and then a list of files.

Any other comments?

Special shout outs to avocados, and stack overflow!

from @scaramallion 's comment I would like to start a discussion regarding best practices.

contributing guide:

Do you have any objection to adopting this contributing guide from scikit-learn (either partially or fully)

Merge policy:

I would propose a policy of MRG+2. Maybe we should rework the pydicom rights. We could keep that only @darcymason, @scaramallion and @vsoch could merge to master (as it is, right now) but allow other people from pydicom edit the issue tracker (to +1 PR, close Issues, manage tags, etc..). Maybe we could also add @rhaxton and @glemaitre in such category, if they want to.

From [email protected] on October 07, 2008 20:40:33

pydicom can read JPEG files, but the pixel data remains compressed. Should investigate incorporating JPEG code to allow at least decompression of read images.

Original issue: http://code.google.com/p/pydicom/issues/detail?id=16

The 1.4 release is scheduled for December, so we may start to prepare it, especially regarding the issues to be fixed for the release.

Release check list (more information)

• [x] go through issues and close, assign to this version, or assign to future versions
• [x] go through PRs to see which can be pulled in before release
• [x] update Release Notes by going through revision history
• [x] update the version in pydicom/_version.py to release
• [x] check in the changes and create a branch and a GitHub release
• [x] get the new DOI at https://zenodo.org/account/settings/github/repository/pydicom/pydicom), and update the README.md in the release branch
• [x] publish on PyPi
• [x] update documentation version on GitHub Pages
• [x] update the version in pydicom/_version.py in master to next development version (major.minor.0.dev0), and update the DOI in the README.md
• [x] merge auto-generated PR in conda-forge pydicom-feedstock
• [ ] announce on pydicom google group

List of issues tagged for 1.4 release

(with my usual 2 € cents added)

• [x] ~#881 File_meta - there is ongoing work on that in #885 by @darcymason~ v2.0
• [x] ~#148 Error when write dicom with Ironpython: this is difficult without pytest working there, not sure who can handle this~ - closed as not a bug
• [x] #277 Programmatically Find Corrupt Files: this is about propagating an EOF exception in strict mode, trivial fix if wanted :heavy_check_mark:
• [x] #285 Document use of Datasets without files: probably just another small example in the documentation, can be easily done :heavy_check_mark:
• [x] #456 performance/time_tests has hardcoded paths: not really important, best done by @darcymason as he uses this code, but milestone can easily be moved :heavy_check_mark:
• [x] #483 Difference of data_element_generator in filereader and util.leandread: this needs only a docstring update, so can be done easily :heavy_check_mark:
• [x] #537 Choose image handlers explicitly: given the trouble with different handlers, this would be helpful, I think - @darcymason, can you check if your last suggestion is still valid? :heavy_check_mark:
• [x] #685 Generators in encaps don't handle single fragment per frame correctly with no BOT value - there is a rather old PR #688 - handled by @scaramallion - new PR #997 ✔️
• [x] #693 Wrong jpeg 2000 image from pillow handler - PR #1001 ✔️
• [x] ~#790 Clarify pydicom-contrib versus examples in pydicom: this is a request for discussion, that makes sense, but is not relevant for the release IMHO~ - removed milestone
• [x] #822 Handling DICOMDIR files with records in reverse-hierarchical order: trivial fix, ~I actually did this some time ago~ - confused this with another issue, but the fix has been provided, it is merely a matter of finding/generating test data, maybe I will have a look :heavy_check_mark:
• [x] ~#826 Wrong RGB values when using pixel_array: unclear, probably a Pillow issue, and missing feedback - would remove this from the list~ addressed via documentation - s
• [x] #848 Dicomdir should warn if not explicit VR little endian - easily done :heavy_check_mark:
• [x] PR #824 / #1012 Implementation of structured reporting ✔️

Description

I created a dicom file in pydicom,
I used the code to write. I wrote the dicom file in pydicom as that message and it is showed in pydicom as follow: The dicom file just 79 kb, I don't know how to get a correct format. Please help me,thanks code:

    file_meta = Dataset()
    file_meta.MediaStorageSOPClassUID = RS_SOPInstanceUID
    file_meta.MediaStorageSOPInstanceUID = "RT Structure Set Storage"
    file_meta.TransferSyntaUID='Explicit VR Little Endian'
    file_meta.ImplementationClassUID = "1.2.250.1.59.3.0.3.3.1"
    RT_imageStorage = FileDataset(save_path, {},
                 file_meta=file_meta, preamble=b"\0" * 128)
    RT_imageStorage.SpecificCharacterSet=CT.SpecificCharacterSet
    RT_imageStorage.InstanceCreationDate=InstanceCreationDate
    RT_imageStorage.InstanceCreationTime=InstanceCreationTime
    RT_imageStorage.SOPClassUID='RT Structure Set Storage'
    RT_imageStorage.SOPInstanceUID= RS_SOPInstanceUID
    RT_imageStorage.StudyDate=CT.StudyDate
    RT_imageStorage.StudyTime=CT.StudyTime
    RT_imageStorage.AccessionNumber=''
    RT_imageStorage.Modality='RTSTRUCT
    RT_imageStorage.is_little_endian = False
    RT_imageStorage.is_implicit_VR = False
    RT_imageStorage.save_as('/public/home/write2dcm/123/test/1234.dcm')'

(3006, 002a) ROI Display Color IS: ['0', '147', '0'] (3006, 0040) Contour Sequence 12 item(s) ---- (3006, 0016) Contour Image Sequence 1 item(s) ---- (0008, 1150) Referenced SOP Class UID UI: CT Image Storage (0008, 1155) Referenced SOP Instance UID UI: 1.3.6.1.4.1.2452.6.3054396209.xxxxxxxx.1983321519.xxxxxxxxx --------- (3006, 0042) Contour Geometric Type CS: 'CLOSED_PLANAR' (3006, 0046) Number of Contour Points IS: "58" (3006, 0048) Contour Number IS: "1" (3006, 0050) Contour Data DS: ['24.671679', '-57.148172', '31.000000', '25.532824', '-57.054517', '31.000000', '26.378794', '-56.868305', '31.000000', '27.199673', '-56.591719', '31.000000', '27.985835', '-56.228001', '31.000000', '28.728064', '-55.781417', '31.000000', '29.417658', '-55.257201', '31.000000', '30.046531', '-54.661501', '31.000000', '30.607312', '-54.001299', '31.000000', '31.093425', '-53.284336', '31.000000', '31.499171', '-52.519018', '31.000000', '31.819793', '-51.714317', '31.000000', '32.051532', '-50.879669', '31.000000', '32.191671', '-50.024857', '31.000000', '32.238568', '-49.159905', '31.000000', '32.191671', '-48.294953', '31.000000', '32.051532', '-47.440141', '31.000000', '31.819793', '-46.605493', '31.000000', '31.499171', '-45.800792', '31.000000', '31.093425', '-45.035474', '31.000000', '30.607312', '-44.318511', '31.000000', '30.046531', '-43.658309', '31.000000', '29.417658', '-43.062609', '31.000000', '28.728064', '-42.538393', '31.000000', '27.985835', '-42.091809', '31.000000', '27.199673', '-41.728091', '31.000000', '26.378794', '-41.451505', '31.000000', '25.532824', '-41.265293', '31.000000', '24.671679', '-41.171638', '31.000000', '23.805456', '-41.171638', '31.000000', '22.944312', '-41.265293', '31.000000', '22.098341', '-41.451505', '31.000000', '21.277462', '-41.728091', '31.000000', '20.491300', '-42.091809', '31.000000', '19.749071', '-42.538393', '31.000000', '19.059477', '-43.062609', '31.000000', '18.430604', '-43.658309', '31.000000', '17.869823', '-44.318511', '31.000000', '17.383710', '-45.035474', '31.000000', '16.977964', '-45.800792', '31.000000', '16.657342', '-46.605493', '31.000000', '16.425603', '-47.440141', '31.000000', '16.285464', '-48.294953', '31.000000', '16.238568', '-49.159905', '31.000000', '16.285464', '-50.024857', '31.000000', '16.425603', '-50.879669', '31.000000', '16.657342', '-51.714317', '31.000000', '16.977964', '-52.519018', '31.000000', '17.383710', '-53.284336', '31.000000', '17.869823', '-54.001299', '31.000000', '18.430604', '-54.661501', '31.000000', '19.059477', '-55.257201', '31.000000', '19.749071', '-55.781417', '31.000000', '20.491300', '-56.228001', '31.000000', '21.277462', '-56.591719', '31.000000', '22.098341', '-56.868305', '31.000000', '22.944312', '-57.054517', '31.000000', '23.805456', '-57.148172', '31.000000']

Steps/Code to Reproduce

Expected Results

Actual Results

Versions

Can we get a pypi release of pydicom with the new package name? The fact you cannot install from pypi with the new package name is causing issues like: https://github.com/patmun/pynetdicom/pull/43.

related to #383 closes #366

This PR intends:

• [x] Build with Circle CI
• [x] Automatic examples generation using sphinx-gallery
• [x] Use numpydoc
• [x] Clean the install with only the necessary packages
• [ ] Generate and add pair of SSH keys for deploying doc
• [x] Initialize the gh-pages with the folder structure. #389

Hi Everyone,

i have a directory with 189 DICOM data and i want to extract all the pixel Value in a specific ROI from all the DICOM Images , i used to do this for one image and that´s working. i tried to open the directory and to switch it into numpy Array but i couldnt have any results.

This how looks my first try:

import os import pydicom import matplotlib.pyplot as plt import numpy as np

dirname = 'C:\Python27\DICOM\ST000000\SE000013/' files = os.listdir(dirname) ds_list = [pydicom.dcmread(os.path.join(dirname, filename) ) for filename in files]

Thanks !

Is your feature request related to a problem? Please describe. The problem is that using pixel_array is very slow with very large images. GPU based Libraries like nvjpeg and nvjpeg2000 https://developer.nvidia.com/nvjpeg exist which speed up this process immensely. It'd be great to have an api with pydicom which can extract the underlying jpg file directly to a stream or to a file which can be loaded via tools like dali. https://developer.nvidia.com/dali

Describe the solution you'd like something like ds.to_underlying_jpg("file.jpg") without doing any handler decoding.

Describe the bug

2 TestFileSet tests fail on i686 (32-bit x86) architecture with an OverflowError. FAILED pydicom/tests/test_fileset.py::TestFileSet_Modify::test_write_file_id FAILED pydicom/tests/test_fileset.py::TestFileSet_Copy::test_file_id

Expected behavior

Test behavior should be consistent across architectures.

Steps To Reproduce

Run

pytest pydicom/tests/test_fileset.py 

in the pydicom directory on an i686 machine. Virtualizing i686 using QEMU also reproduces the issue.

=================================== FAILURES ===================================
____________________ TestFileSet_Modify.test_write_file_id _____________________

self = <pydicom.tests.test_fileset.TestFileSet_Modify object at 0xe87f1430>
tiny = Dataset.file_meta -------------------------------
(0002, 0000) File Meta Information Group Length  UL: 200
(0002, 0001...Syntax UID in F UI: Explicit VR Little Endian
   (0020, 0013) Instance Number                     IS: '49'
   ---------

    def test_write_file_id(self, tiny):
        """Test that the File IDs character sets switch correctly."""
        tdir, ds = temporary_fs(tiny)
    
        def my_len(self):
            return 10**6 + 1
    
        FileSet.__len__ = my_len
        fs = FileSet(ds)
        assert 10**6 + 1 == len(fs)
        ds, paths = write_fs(fs)
        instance = fs._instances[-1]
        # Was written with alphanumeric File IDs
        assert "IM00001D" in instance.path
    
        def my_len(self):
            return 36**6 + 1
    
        FileSet.__len__ = my_len
        fs = FileSet(ds)
>       assert 36**6 + 1 == len(fs)
E       OverflowError: cannot fit 'int' into an index-sized integer

pydicom/tests/test_fileset.py:2249: OverflowError
________________________ TestFileSet_Copy.test_file_id _________________________

self = <pydicom.tests.test_fileset.TestFileSet_Copy object at 0xe837f370>
tiny = Dataset.file_meta -------------------------------
(0002, 0000) File Meta Information Group Length  UL: 200
(0002, 0001...Syntax UID in F UI: Explicit VR Little Endian
   (0020, 0013) Instance Number                     IS: '49'
   ---------
tdir = <TemporaryDirectory '/tmp/guix-build-python-pydicom-2.3.1.drv-0/tmpcki9joul'>

    def test_file_id(self, tiny, tdir):
        """Test that the File IDs character sets switch correctly."""
        def my_len(self):
            return 10**6 + 1
    
        FileSet.__len__ = my_len
        fs = FileSet(tiny)
        assert 10**6 + 1 == len(fs)
        fs, ds, paths = copy_fs(fs, tdir.name)
        instance = fs._instances[-1]
        # Was written with alphanumeric File IDs
        assert "IM00001D" in instance.path
    
        def my_len(self):
            return 36**6 + 1
    
        FileSet.__len__ = my_len
        fs = FileSet(tiny)
>       assert 36**6 + 1 == len(fs)
E       OverflowError: cannot fit 'int' into an index-sized integer

pydicom/tests/test_fileset.py:2580: OverflowError

Your environment

module       | version
------       | -------
platform     | Linux-6.0.7-i686-with-glibc2.33
Python       | 3.9.9 (main, Jan  1 1970, 00:00:01)  [GCC 10.3.0]
pydicom      | 2.3.1
gdcm         | _module not found_
jpeg_ls      | _module not found_
numpy        | 1.21.6
PIL          | 9.2.0
pylibjpeg    | _module not found_
openjpeg     | _module not found_
libjpeg      | _module not found_

Hello! I came across this problem with a particular DICOM file. The 0002,0010 tag occurs twice in the dataset.

If you do:

ds = pydicom.dcmread('badTSUID.dcm')
print(ds.file_meta.TransferSyntaxUID)

The output will be:

1.2.840.10008.1.2.1

If you do:

del ds.file_meta.TransferSyntaxUID

Both of the tags are deleted.

In this particular case the one that's in the file meta should be trusted. I could use the del to delete them both and rewrite, but to do that I need to know the value of the tag in Meta to write the correct one. I am not sure how to deal with this kind of cases correctly. I've attached the anonymized dataset to this message. Thank you! badTSUID.zip

Describe the bug There is a file = filename The filename tag SpecificCharacterSet = ISO_IR 144

ds = dcmread(filename) ds.decode() ds['SpecificCharacterSet'].value = 'ISO_IR 192' ds.save_as(fileout)

Causes an exception: UnicodeEncodeError: 'latin-1' codec can't encode character '\u044d' in position 0: ordinal not in range(256)

I understand that there is the wrong symbol somewhere in the tags causing the exception but I dunno where.

Doing:

ds = dcmread(filename) ds.save_as(fileout)

Causes no error.

What is the best way to catch exceptions like this one? It's totally unpredictable in my datasets.

The codify engine will produce code with incorrect AT values:

from pydicom import Dataset
from pydicom.util.codify import code_dataset

ds = Dataset()
ds.OffendingElement = (0x00aa, 0x00bb)

print(code_dataset(ds))

gives output:

ds = Dataset()
ds.OffendingElement = (00aa, 00bb)

It is missing the leading "0x" on each value to indicate they are hex. In this case, it generates a syntax error; in some cases it could pass but be incorrect, if there were no leading 00's and no letter characters in the hex numbers.

Describe the bug When importing pydicom with a multi process program, a circular import happens. The stack trace is the following:

multiprocessing.managers.RemoteError: 
---------------------------------------------------------------------------
Traceback (most recent call last):
  File "/usr/lib/python3.8/multiprocessing/managers.py", line 243, in serve_client
    request = recv()
  File "/usr/lib/python3.8/multiprocessing/connection.py", line 251, in recv
    return _ForkingPickler.loads(buf.getbuffer())
  File "/home/romain/Documents/.env/lib/python3.8/site-packages/pydicom/__init__.py", line 35, in <module>
    from pydicom.filewriter import dcmwrite, write_file
  File "/home/romain/Documents/.env/lib/python3.8/site-packages/pydicom/filewriter.py", line 23, in <module>
    from pydicom.values import convert_numbers
  File "/home/romain/Documents/.env/lib/python3.8/site-packages/pydicom/values.py", line 621, in <module>
    ) -> Union[pydicom.uid.UID, SequenceType[pydicom.uid.UID]]:
AttributeError: partially initialized module 'pydicom' has no attribute 'uid' (most likely due to a circular import)
---------------------------------------------------------------------------

The error occurs in multiple process, sometimes with the following:

  File "/home/romain/Documents/.env/lib/python3.8/site-packages/pydicom/dataelem.py", line 31, in <module>
    from pydicom.valuerep import PersonName
ImportError: cannot import name 'PersonName' from partially initialized module 'pydicom.valuerep' (most likely due to a circular import)

Expected behavior The import should take place without error.

Steps To Reproduce The bug is hard to reproduce, I'm using a library that I can't share, but we only do a import pydicom. I have not been able to reproduce the bug in a simple way for it to happen every time, it can be random or occur every time when changing an unrelated file. If anyone has an idea to reproduce it, I'm willing to try.

Your environment module | version ------ | ------- platform | Linux-5.10.16.3-microsoft-standard-WSL2-x86_64-with-glibc2.29 Python | 3.8.10 (default, Jun 22 2022, 20:18:18) [GCC 9.4.0] pydicom | 2.1.2 gdcm | module not found jpeg_ls | module not found numpy | 1.22.3 PIL | 9.0.1