Skip to content
Merged
Show file tree
Hide file tree
Changes from all commits
Commits
File filter

Filter by extension

Filter by extension

Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
2 changes: 1 addition & 1 deletion docs/coding.rst
Original file line number Diff line number Diff line change
Expand Up @@ -79,7 +79,7 @@ value in `pydicom`:

tumor_code = codes.SCT.Tumor
print(tumor_code.value)
# '1083690006'
# '108369006'
print(tumor_code.scheme_designator)
# 'SCT'
print(tumor_code.meaning)
Expand Down
2 changes: 1 addition & 1 deletion docs/development.rst
Original file line number Diff line number Diff line change
Expand Up @@ -23,7 +23,7 @@ Pull requests

We encourage contributions from the users of the library (provided that they fit within the scope of the project).

If you are planning to make a contribution to the library, we encourage you to leave an issue first on the `issue tracker <https://github.com/ImagingDataCommons/higdicom/issues>`_ detailing your proposed contribution.
If you are planning to make a contribution to the library, we encourage you to leave an issue first on the `issue tracker <https://github.com/ImagingDataCommons/highdicom/issues>`_ detailing your proposed contribution.
This way, the maintainers can vet your proposal, make sure it is within the scope of the project, and guide you through the process of creating a successful pull request.
Before creating a pull request on Github, read the coding style guideline, run the tests and check PEP8 compliance.

Expand Down
6 changes: 3 additions & 3 deletions docs/generalsr.rst
Original file line number Diff line number Diff line change
Expand Up @@ -9,10 +9,10 @@ supports structured reports through the :mod:`highdicom.sr` sub-package.

SRs are highly complex, and this page attempts to give a basic introduction
while also describing the implementation within `highdicom`. A more thorough
explanation my be found in:
explanation may be found in:

* *DICOM Structured Reporting*. David Clunie. PixelMed Publishing, 2000.
Digital copy available
Digital copy available
`here <https://www.dclunie.com/pixelmed/DICOMSR.book.pdf>`_.

Content Items
Expand Down Expand Up @@ -53,7 +53,7 @@ item. The classes representing these content items in `highdicom` are:
- :class:`highdicom.sr.UIDRefContentItem`: The value is a UID (unique
identifier).

These classes are all subclasses pf ``pydicom.Dataset`` and you can view and
These classes are all subclasses of ``pydicom.Dataset`` and you can view and
interact with their attributes as you can with any pydicom dataset.

You can look at the API for each class to see how to construct content items of
Expand Down
2 changes: 1 addition & 1 deletion docs/image.rst
Original file line number Diff line number Diff line change
Expand Up @@ -72,7 +72,7 @@ frames of the image:
(see :doc:`pixel_transforms` for more details on pixel transforms), but by
default any pixel transform found in the dataset except the value-of-interest
(VOI) transform is applied. This should be your default way of accessing
image frames in most cases, since it will typtically return the pixels as the
image frames in most cases, since it will typically return the pixels as the
creator of the object intended them to be understood. By default, the
returned frames have datatype ``numpy.float64``, but this can be controlled
using the ``dtype`` parameter.
Expand Down
4 changes: 2 additions & 2 deletions docs/release_notes.rst
Original file line number Diff line number Diff line change
Expand Up @@ -113,13 +113,13 @@ systems, which are shifted by 0.5 pixels.
1. **Pixel indices**: (column, row) indices into the pixel matrix. The values
are zero-based integers in the range [0, Columns - 1] and [0, Rows - 1].
Pixel indices are defined relative to the centers of pixels and the (0, 0)
index is located at the center of the top left corner hand pixel of the
index is located at the center of the top left corner pixel of the
total pixel matrix.
2. **Image coordinates**: (column, row) coordinates in the pixel matrix at
sub-pixel resolution. The values are floating-point numbers in the range
[0, Columns] and [0, Rows]. Image coordinates are defined relative to the
top left corner of the pixels and the (0.0, 0.0) point is located at the top
left corner of the top left corner hand pixel of the total pixel matrix.
left corner of the top left corner pixel of the total pixel matrix.

To account for these differences, introduced two additional transformer classes
in highdicom 0.14.1. and made changes to the existing ones.
Expand Down
6 changes: 3 additions & 3 deletions docs/remote.rst
Original file line number Diff line number Diff line change
Expand Up @@ -59,7 +59,7 @@ spatial patch from a large whole slide image from the IDC.
with blob.open(mode="rb", chunk_size=500_000) as reader:
im = hd.imread(reader, lazy_frame_retrieval=True)

# Grab an arbitrary region of tile full pixel matrix
# Grab an arbitrary region of the full pixel matrix
region = im.get_total_pixel_matrix(
row_start=15000,
row_end=15512,
Expand Down Expand Up @@ -163,11 +163,11 @@ the ``s3fs`` documentation for details).
# URL to a whole slide image from the IDC "CCDS MCI" collection on AWS S3
url = 's3://idc-open-data/763fe058-7d25-4ba7-9b29-fd3d6c41dc4b/210f0529-c767-4795-9acf-bad2f4877427.dcm'

# Read the imge directly from the blob
# Read the image directly from the blob
with s3_client.open(url, mode="rb") as reader:
im = hd.imread(reader, lazy_frame_retrieval=True)

# Grab an arbitrary region of tile full pixel matrix
# Grab an arbitrary region of the full pixel matrix
region = im.get_total_pixel_matrix(
row_start=15000,
row_end=15512,
Expand Down
2 changes: 1 addition & 1 deletion docs/seg.rst
Original file line number Diff line number Diff line change
Expand Up @@ -53,7 +53,7 @@ are numbered with consecutive segment numbers starting at 1 (i.e., 1, 2, 3,
...). Additionally, each segment present is accompanied by information
describing what the segment represents. This information is placed in the
"SegmentsSequence" (0062, 0002) attribute of the segmentation file. In
*highdcom*, we use the :class:`highdicom.seg.SegmentDescription` class to hold
*highdicom*, we use the :class:`highdicom.seg.SegmentDescription` class to hold
this information. This is not to be confused with the DICOM "Segment
Description" attribute, which is a plain text string. When you construct a
DICOM SEG image using *highdicom*, you must construct a single
Expand Down
12 changes: 6 additions & 6 deletions docs/tid1500.rst
Original file line number Diff line number Diff line change
Expand Up @@ -4,7 +4,7 @@ The TID1500 Measurement Report Template
=======================================

The `TID1500 "Measurement Report" <tid1500def_>`_ template is a general-purpose
template for communicating measurements and qualitative qualitative evaluations
template for communicating measurements and qualitative evaluations
derived from one or more images or regions of images. It is recommended to read
the previous page on :ref:`generalsr` before this page.

Expand Down Expand Up @@ -460,7 +460,7 @@ type (some have been omitted for brevity):
- ``measurements``: (Sequence of :class:`highdicom.sr.Measurement`, optional)
Numeric measurements
- ``qualitative_evaluations``: (Sequence of :class:`highdicom.sr.CodedConcept`, optional)
Coded name-value pairs that describe qualitative qualitative_evaluations
Coded name-value pairs that describe qualitative evaluations
- ``finding_category``: (:class:`highdicom.sr.CodedConcept`, optional)
Category of observed finding, e.g., anatomic structure or
morphologically abnormal structure
Expand All @@ -482,7 +482,7 @@ Qualitative Evaluations
A Qualitative Evaluation is essentially a categorical value inferred from an
image. For example, this could represent a diagnosis derived from the
referenced region or a severity grading. These are represented in *highdicom*
using the class :class:`highdicom.sr.QualitativeEvalution`, which is
using the class :class:`highdicom.sr.QualitativeEvaluation`, which is
essentially a single :class:`highdicom.sr.CodeContentItem` within a special
template.

Expand All @@ -495,15 +495,15 @@ parameters as coded values:
from pydicom.sr.codedict import codes

# An evaluation of disease severity as "mild"
severity_item = hd.sr.QualitativeEvalution(
severity_item = hd.sr.QualitativeEvaluation(
name=codes.SCT.Severity,
value=codes.SCT.Mild,
)

# An evaluation of tumor morphology as adenocarcinoma
morphology_item = hd.sr.QualitativeEvalution(
morphology_item = hd.sr.QualitativeEvaluation(
name=codes.SCT.AssociatedMorphology,
value=codes.SCT.Anenocarcinoma,
value=codes.SCT.Adenocarcinoma,
)

Measurements (`TID300 <tid300def_>`_)
Expand Down
2 changes: 1 addition & 1 deletion docs/tid1500parsing.rst
Original file line number Diff line number Diff line change
Expand Up @@ -233,7 +233,7 @@ A volumetric group returns a :class:`highdicom.sr.VolumeSurface` or list of
:class:`highdicom.sr.ImageRegion` objects, depending on the reference type. If
instead, a planar/volumetric measurement group uses the ``ReferencedSegment``
reference type, the referenced segment can be accessed by the
``group.referenced_segmention_frame`` property (for planar groups) or
``group.referenced_segmentation_frame`` property (for planar groups) or
``group.referenced_segment`` property (for volumetric groups), which return
objects of type :class:`highdicom.sr.ReferencedSegmentationFrame` and
:class:`highdicom.sr.ReferencedSegment` respectively.
Expand Down
2 changes: 1 addition & 1 deletion docs/volume.rst
Original file line number Diff line number Diff line change
Expand Up @@ -81,7 +81,7 @@ to "LPS" convention for you.

The top-left 3x3 matrix of the affine matrix consists of three orthogonal
column vectors that give the vector travelled when incrementing the voxel
indices in each o the three dimensions. The top three elements of the last
indices in each of the three dimensions. The top three elements of the last
column give the position of the voxel at index ``(0, 0, 0)``. The bottom row is
always ``[0., 0., 0., 1.]``. The :meth:`highdicom.Volume.from_components()`
method allows you to construct a volume by specifying these components of the
Expand Down
2 changes: 1 addition & 1 deletion examples/README.md
Original file line number Diff line number Diff line change
Expand Up @@ -11,4 +11,4 @@ docker build . -t highdicom/examples:latest
docker run --rm --name highdicom_examples -p 8888:8888 highdicom/examples:latest
```

After running the above commands, following the instructions printed into the standard output stream to access the notebooks in your browser.
After running the above commands, follow the instructions printed into the standard output stream to access the notebooks in your browser.