Updating the docs in dev/ for branch: main, commit 4bc3d1f [skip ci]

dev/.buildinfo

@@ -1,4 +1,4 @@
 # Sphinx build info version 1
 # This file hashes the configuration used when building these files. When it is not found, a full rebuild will be done.
-config: c2d5ab8c786e2ae26548a1d2bd787279
+config: 84dae121a1cb36b11e1fea060103c0d3
 tags: 645f666f9bcd5a90fca523b33c5a78b7

dev/_sources/auto_examples/image_processing/plot_downsize_image.rst.txt

@@ -168,7 +168,7 @@ instead of averagin the pixels. Finally, the image is store as a dicom image.
 
 .. rst-class:: sphx-glr-timing
 
-   **Total running time of the script:** (0 minutes 0.006 seconds)
+   **Total running time of the script:** (0 minutes 0.005 seconds)
 
 
 .. _sphx_glr_download_auto_examples_image_processing_plot_downsize_image.py:

dev/_sources/auto_examples/image_processing/plot_waveforms.rst.txt

@@ -85,7 +85,7 @@ matplotlib.
 
 .. rst-class:: sphx-glr-timing
 
-   **Total running time of the script:** (0 minutes 0.266 seconds)
+   **Total running time of the script:** (0 minutes 0.212 seconds)
 
 
 .. _sphx_glr_download_auto_examples_image_processing_plot_waveforms.py:

dev/_sources/auto_examples/image_processing/sg_execution_times.rst.txt

@@ -6,7 +6,7 @@
 
 Computation times
 =================
-**00:00.271** total execution time for 3 files **from auto_examples/image_processing**:
+**00:00.218** total execution time for 3 files **from auto_examples/image_processing**:
 
 .. container::
 
@@ -33,10 +33,10 @@ Computation times
      - Time
      - Mem (MB)
    * - :ref:`sphx_glr_auto_examples_image_processing_plot_waveforms.py` (``plot_waveforms.py``)
-     - 00:00.266
+     - 00:00.212
      - 0.0
    * - :ref:`sphx_glr_auto_examples_image_processing_plot_downsize_image.py` (``plot_downsize_image.py``)
-     - 00:00.006
+     - 00:00.005
      - 0.0
    * - :ref:`sphx_glr_auto_examples_image_processing_reslice.py` (``reslice.py``)
      - 00:00.000

dev/_sources/auto_examples/input_output/plot_read_dicom.rst.txt

@@ -95,7 +95,7 @@ information, and show it using matplotlib.
 
 .. rst-class:: sphx-glr-timing
 
-   **Total running time of the script:** (0 minutes 0.093 seconds)
+   **Total running time of the script:** (0 minutes 0.085 seconds)
 
 
 .. _sphx_glr_download_auto_examples_input_output_plot_read_dicom.py:

dev/_sources/auto_examples/input_output/plot_read_fileset.rst.txt

@@ -105,7 +105,7 @@ This example shows how to read and interact with a DICOM File-set.
     Found 0 instances with PhotometricInterpretation='MONOCHROME1' without loading the stored instances and 3 instances with loading
 
     Original File-set still at /root/project/src/pydicom/data/test_files/dicomdirtests
-    File-set copied to /tmp/tmpdepmqixn and contains the following files:
+    File-set copied to /tmp/tmp41n5ppku and contains the following files:
       DICOMDIR
       PT000000/ST000000/SE000000/IM000000
       PT000000/ST000000/SE000001/IM000000
@@ -264,7 +264,7 @@ This example shows how to read and interact with a DICOM File-set.
 
 .. rst-class:: sphx-glr-timing
 
-   **Total running time of the script:** (0 minutes 0.331 seconds)
+   **Total running time of the script:** (0 minutes 0.191 seconds)
 
 
 .. _sphx_glr_download_auto_examples_input_output_plot_read_fileset.py:

dev/_sources/auto_examples/input_output/plot_write_dicom.rst.txt

@@ -37,8 +37,8 @@ have to change UIDs to valid values and add all required DICOM data elements.
 
     Setting dataset values...
     Setting file meta information...
-    Writing dataset to: /tmp/tmph4oxyzvs.dcm
-    Load dataset from: /tmp/tmph4oxyzvs.dcm ...
+    Writing dataset to: /tmp/tmpgybbis0a.dcm
+    Load dataset from: /tmp/tmpgybbis0a.dcm ...
     Dataset.file_meta -------------------------------
     (0002,0000) File Meta Information Group Length  UL: 128
     (0002,0001) File Meta Information Version       OB: b'\x00\x01'
@@ -48,11 +48,11 @@ have to change UIDs to valid values and add all required DICOM data elements.
     (0002,0012) Implementation Class UID            UI: 1.2.3.4
     (0002,0013) Implementation Version Name         SH: 'PYDICOM 3.0.0'
     -------------------------------------------------
-    (0008,0023) Content Date                        DA: '20240401'
-    (0008,0033) Content Time                        TM: '170052.488931'
+    (0008,0023) Content Date                        DA: '20240406'
+    (0008,0033) Content Time                        TM: '213624.606505'
     (0010,0010) Patient's Name                      PN: 'Test^Firstname'
     (0010,0020) Patient ID                          LO: '123456'
-    Deleting file: /tmp/tmph4oxyzvs.dcm ...
+    Deleting file: /tmp/tmpgybbis0a.dcm ...
 
 
 
@@ -112,7 +112,7 @@ have to change UIDs to valid values and add all required DICOM data elements.
 
 .. rst-class:: sphx-glr-timing
 
-   **Total running time of the script:** (0 minutes 0.005 seconds)
+   **Total running time of the script:** (0 minutes 0.004 seconds)
 
 
 .. _sphx_glr_download_auto_examples_input_output_plot_write_dicom.py:

dev/_sources/auto_examples/input_output/sg_execution_times.rst.txt

@@ -6,7 +6,7 @@
 
 Computation times
 =================
-**00:00.437** total execution time for 5 files **from auto_examples/input_output**:
+**00:00.287** total execution time for 5 files **from auto_examples/input_output**:
 
 .. container::
 
@@ -33,16 +33,16 @@ Computation times
      - Time
      - Mem (MB)
    * - :ref:`sphx_glr_auto_examples_input_output_plot_read_fileset.py` (``plot_read_fileset.py``)
-     - 00:00.331
+     - 00:00.191
      - 0.0
    * - :ref:`sphx_glr_auto_examples_input_output_plot_read_dicom.py` (``plot_read_dicom.py``)
-     - 00:00.093
+     - 00:00.085
      - 0.0
    * - :ref:`sphx_glr_auto_examples_input_output_plot_printing_dataset.py` (``plot_printing_dataset.py``)
      - 00:00.005
      - 0.0
    * - :ref:`sphx_glr_auto_examples_input_output_plot_write_dicom.py` (``plot_write_dicom.py``)
-     - 00:00.005
+     - 00:00.004
      - 0.0
    * - :ref:`sphx_glr_auto_examples_input_output_plot_read_rtplan.py` (``plot_read_rtplan.py``)
      - 00:00.003

dev/_sources/auto_examples/metadata_processing/plot_anonymize.rst.txt

@@ -207,7 +207,7 @@ Finally, this is possible to store the image
 
 .. rst-class:: sphx-glr-timing
 
-   **Total running time of the script:** (0 minutes 0.011 seconds)
+   **Total running time of the script:** (0 minutes 0.007 seconds)
 
 
 .. _sphx_glr_download_auto_examples_metadata_processing_plot_anonymize.py:

dev/_sources/auto_examples/metadata_processing/plot_sequences.rst.txt

@@ -81,7 +81,7 @@ This examples illustrates how to work with sequences.
 
 .. rst-class:: sphx-glr-timing
 
-   **Total running time of the script:** (0 minutes 0.002 seconds)
+   **Total running time of the script:** (0 minutes 0.001 seconds)
 
 
 .. _sphx_glr_download_auto_examples_metadata_processing_plot_sequences.py:

dev/_sources/auto_examples/metadata_processing/sg_execution_times.rst.txt

@@ -6,7 +6,7 @@
 
 Computation times
 =================
-**00:00.016** total execution time for 3 files **from auto_examples/metadata_processing**:
+**00:00.011** total execution time for 3 files **from auto_examples/metadata_processing**:
 
 .. container::
 
@@ -33,11 +33,11 @@ Computation times
      - Time
      - Mem (MB)
    * - :ref:`sphx_glr_auto_examples_metadata_processing_plot_anonymize.py` (``plot_anonymize.py``)
-     - 00:00.011
+     - 00:00.007
      - 0.0
    * - :ref:`sphx_glr_auto_examples_metadata_processing_plot_add_dict_entries.py` (``plot_add_dict_entries.py``)
      - 00:00.003
      - 0.0
    * - :ref:`sphx_glr_auto_examples_metadata_processing_plot_sequences.py` (``plot_sequences.py``)
-     - 00:00.002
+     - 00:00.001
      - 0.0

dev/_sources/auto_examples/plot_dicom_difference.rst.txt

@@ -742,7 +742,7 @@ This examples illustrates how to find the differences between two DICOM files.
 
 .. rst-class:: sphx-glr-timing
 
-   **Total running time of the script:** (0 minutes 0.106 seconds)
+   **Total running time of the script:** (0 minutes 0.096 seconds)
 
 
 .. _sphx_glr_download_auto_examples_plot_dicom_difference.py:

dev/_sources/auto_examples/sg_execution_times.rst.txt

@@ -6,7 +6,7 @@
 
 Computation times
 =================
-**00:00.106** total execution time for 4 files **from auto_examples**:
+**00:00.096** total execution time for 4 files **from auto_examples**:
 
 .. container::
 
@@ -33,7 +33,7 @@ Computation times
      - Time
      - Mem (MB)
    * - :ref:`sphx_glr_auto_examples_plot_dicom_difference.py` (``plot_dicom_difference.py``)
-     - 00:00.106
+     - 00:00.096
      - 0.0
    * - :ref:`sphx_glr_auto_examples_dicomtree.py` (``dicomtree.py``)
      - 00:00.000

dev/_sources/guides/encoding/jpeg_2k.rst.txt

@@ -24,8 +24,8 @@ Valid Image Pixel Parameters
 ----------------------------
 
 The table below lists the valid :dcm:`Image Pixel<part03/sect_C.7.6.3.html>`
-module parameters for *Pixel Data* encoded using *JPEG 2000 Lossless* or *JPEG 2000*
-encoding. For an explanation of each parameter and its relationship
+module parameters for *Pixel Data* encoded using the *JPEG 2000 Lossless* or *JPEG 2000*
+transfer syntaxes. For an explanation of each parameter and its relationship
 with the *Pixel Data* see the :doc:`glossary of Image Pixel elements<../glossary>`.
 
 +------------+-----------------------+-----------------+----------------+------------+---------+

dev/_sources/guides/encoding/jpeg_ls.rst.txt

@@ -12,8 +12,8 @@ Valid Image Pixel Parameters
 ----------------------------
 
 The table below lists the valid :dcm:`Image Pixel<part03/sect_C.7.6.3.html>`
-module parameters for *Pixel Data* encoded using *JPEG-LS Lossless* or *JPEG-LS
-Near-lossless* encoding. For an explanation of each parameter and its relationship
+module parameters for *Pixel Data* encoded using the *JPEG-LS Lossless* or *JPEG-LS
+Near-lossless* transfer syntaxes. For an explanation of each parameter and its relationship
 with the *Pixel Data* see the :doc:`glossary of Image Pixel elements<../glossary>`.
 
 +------------+-----------------------+-----------------+----------------+------------+---------+
@@ -100,7 +100,7 @@ pixel data should already be in the corresponding color space:
 
     * For *Bits Allocated* and *Bits Stored* less than or equal to 8: pixel
       data must be :func:`converted into YCbCr color space
-      <pydicom.pixel_data_handlers.convert_color_space>`. However
+      <pydicom.pixels.processing.convert_color_space>`. However
       you should keep in mind that the conversion operation is lossy.
     * For *Bits Allocated* and *Bits Stored* between 9 and 16 (inclusive):
       pixel data should be downscaled to 8-bit (with *Bits Stored*, *Bits
@@ -113,7 +113,7 @@ pixel data should already be in the corresponding color space:
 
   * For *Photometric Interpretation* ``RGB`` the pixel data must first be
     :func:`converted into RGB color space
-    <pydicom.pixel_data_handlers.convert_color_space>`. However the conversion
+    <pydicom.pixels.processing.convert_color_space>`. However the conversion
     operation is lossy.
   * For *Photometric Interpretation* ``YBR_FULL`` nothing else is required.
 

dev/_sources/guides/encoding/rle_lossless.rst.txt

@@ -12,8 +12,8 @@ Valid Image Pixel Parameters
 ----------------------------
 
 The table below lists the valid :dcm:`Image Pixel<part03/sect_C.7.6.3.html>`
-module parameters for *Pixel Data* encoded using *RLE Lossless* encoding. For
-an explanation of each parameter and its relationship with the
+module parameters for *Pixel Data* encoded using the *RLE Lossless* transfer
+syntax. For an explanation of each parameter and its relationship with the
 *Pixel Data* see the :doc:`glossary of Image Pixel elements<../glossary>`.
 
 +------------+-----------------+-----------------+------------+---------+
@@ -55,7 +55,7 @@ corresponding color space:
 
     * For *Bits Allocated* and *Bits Stored* less than or equal to 8: pixel
       data must be :func:`converted into YCbCr color space
-      <pydicom.pixel_data_handlers.convert_color_space>`. However
+      <pydicom.pixels.processing.convert_color_space>`. However
       you should keep in mind that the conversion operation is lossy.
     * For *Bits Allocated* and *Bits Stored* between 9 and 16 (inclusive):
       pixel data should be downscaled to 8-bit (with *Bits Stored*, *Bits
@@ -68,7 +68,7 @@ corresponding color space:
 
   * For *Photometric Interpretation* ``RGB`` the pixel data must first be
     :func:`converted into RGB color space
-    <pydicom.pixel_data_handlers.convert_color_space>`. However the conversion
+    <pydicom.pixels.processing.convert_color_space>`. However the conversion
     operation is lossy.
   * For *Photometric Interpretation* ``YBR_FULL`` nothing else is required.
 
@@ -153,7 +153,7 @@ new *SOP Instance UID*:
 .. code-block:: python
 
     >>> from pydicom import examples
-    >>> from pydicom.pixel_data_handlers import convert_color_space
+    >>> from pydicom.pixels import convert_color_space
     >>> from pydicom.uid import generate_uid
     >>> ds = examples.rgb_color
     >>> rgb = ds.pixel_array

dev/_sources/old/image_data_compression.rst.txt

@@ -121,7 +121,7 @@ Compressing using third-party packages
 
 If you need to perform pixel data compression using an encoding method not
 supported by *pydicom* - such as :dcm:`ISO/IEC 10918-1 JPEG
-<part05/sect_8.2.html#sect_8.2.1> - then you'll need to find a third-party
+<part05/sect_8.2.html#sect_8.2.1>` - then you'll need to find a third-party
 package or application to do so. Once you've done that you have to follow the
 requirements for compressed *Pixel Data* in the DICOM Standard:
 

dev/_sources/old/working_with_overlays.rst.txt

@@ -68,7 +68,7 @@ overlay pixels start 1 row above and 1 row to the left of the image pixels.
 
 NumPy can be used to modify the pixels, but if the changes are to be saved,
 they must be bit-packed (using something like
-:func:`~pydicom.pixel_data_handlers.numpy_handler.pack_bits`) and written
+:func:`~pydicom.pixels.utils.pack_bits`) and written
 back to the correct element:
 
 .. code-block:: python
@@ -77,7 +77,7 @@ back to the correct element:
   arr[10, :] = 1
 
   # Pack the data
-  from pydicom.pixel_data_handlers.numpy_handler import pack_bits
+  from pydicom.pixels import pack_bits
   packed_bytes = pack_bits(arr)
 
   # Update the element value

dev/_sources/old/working_with_pixel_data.rst.txt

@@ -127,7 +127,7 @@ of ``3`` then the returned pixel data will be in the color space as given by
 
 *pydicom* offers a limited ability to convert between 8-bits/channel YBR and
 RGB color spaces through the
-:func:`~pydicom.pixel_data_handlers.util.convert_color_space`
+:func:`~pydicom.pixels.processing.convert_color_space`
 function. When changing the color space you should also change the value
 of *Photometric Interpretation* to match.
 
@@ -144,13 +144,13 @@ Some DICOM datasets store their output image pixel values in a lookup table
 (LUT), where the values in *Pixel Data* are the index to a corresponding
 LUT entry. When a dataset's (0028,0004) *Photometric Interpretation* value is
 ``PALETTE COLOR`` then the
-:func:`~pydicom.pixel_data_handlers.util.apply_color_lut` function can be used
+:func:`~pydicom.pixels.processing.apply_color_lut` function can be used
 to apply a palette color LUT to the pixel data to produce an RGB image.
 
 .. code-block:: python
 
     from pydicom import examples
-    from pydicom.pixel_data_handlers.util import apply_color_lut
+    from pydicom.pixels import apply_color_lut
 
     # Fetch an example PALETTE COLOR dataset
     ds = examples.palette_color
@@ -165,7 +165,7 @@ of the pixel data is 8-bit.
 .. code-block:: python
 
     from pydicom import examples
-    from pydicom.pixel_data_handlers.util import apply_color_lut
+    from pydicom.pixels import apply_color_lut
 
     ds = examples.palette_color
     arr = ds.pixel_array
@@ -186,7 +186,7 @@ Modality LUT or Rescale Operation
 The DICOM :dcm:`Modality LUT<part03/sect_C.11.html#sect_C.11.1>` module
 converts raw pixel data values to a specific (possibly unitless) physical
 quantity, such as Hounsfield units for CT. The
-:func:`~pydicom.pixel_data_handlers.util.apply_modality_lut` function can be
+:func:`~pydicom.pixels.processing.apply_modality_lut` function can be
 used with an input array of raw values and a dataset containing a Modality LUT
 module to return the converted values. When a dataset requires multiple
 grayscale transformations, the Modality LUT transformation is always applied
@@ -195,7 +195,7 @@ first.
 .. code-block:: python
 
     from pydicom import examples
-    from pydicom.pixel_data_handlers.util import apply_modality_lut
+    from pydicom.pixels import apply_modality_lut
 
     ds = examples.ct
     arr = ds.pixel_array
@@ -207,7 +207,7 @@ VOI LUT or Windowing Operation
 
 The DICOM :dcm:`VOI LUT<part03/sect_C.11.2.html>` module applies a
 VOI or windowing operation to input values. The
-:func:`~pydicom.pixel_data_handlers.util.apply_voi_lut` function
+:func:`~pydicom.pixels.processing.apply_voi_lut` function
 can be used with an input array and a dataset containing a VOI LUT module to
 return values with applied VOI LUT or windowing. When a dataset contains
 multiple VOI or windowing views then a particular view can be returned by
@@ -219,7 +219,7 @@ that the modality LUT or rescale operation has already been applied.
 .. code-block:: python
 
     from pydicom import examples
-    from pydicom.pixel_data_handlers.util import apply_voi_lut
+    from pydicom.pixels import apply_voi_lut
 
     ds = examples.overlay
     arr = ds.pixel_array

dev/_sources/reference/encaps.rst.txt

@@ -3,6 +3,7 @@
 Bulk Data Encapsulation Utilities (:mod:`pydicom.encaps`)
 =========================================================
 
+.. module:: pydicom.encaps
 .. currentmodule:: pydicom.encaps
 
 Functions for parsing and applying encapsulation to bulk data elements such