
.. DO NOT EDIT.
.. THIS FILE WAS AUTOMATICALLY GENERATED BY SPHINX-GALLERY.
.. TO MAKE CHANGES, EDIT THE SOURCE PYTHON FILE:
.. "auto_examples/image_processing/plot_downsize_image.py"
.. LINE NUMBERS ARE GIVEN BELOW.

.. only:: html

    .. note::
        :class: sphx-glr-download-link-note

        :ref:`Go to the end <sphx_glr_download_auto_examples_image_processing_plot_downsize_image.py>`
        to download the full example code.

.. rst-class:: sphx-glr-example-title

.. _sphx_glr_auto_examples_image_processing_plot_downsize_image.py:


================================
Downsize MRI image using pydicom
================================

This example shows how to downsize an MR image from :math:`512  imes 512` to
:math:`64       imes 64`. The downsizing is performed by taking the central section
instead of averagin the pixels. Finally, the image is store as a dicom image.

.. note::

   This example requires the Numpy library to manipulate the pixel data.

.. GENERATED FROM PYTHON SOURCE LINES 15-42




.. rst-class:: sphx-glr-script-out

 .. code-block:: none


    The image has 64 x 64 voxels
    The downsampled image has 8 x 8 voxels
    The information of the data set after downsampling: 

    Dataset.file_meta -------------------------------
    (0002,0000) File Meta Information Group Length  UL: 190
    (0002,0001) File Meta Information Version       OB: b'\x00\x01'
    (0002,0002) Media Storage SOP Class UID         UI: MR Image Storage
    (0002,0003) Media Storage SOP Instance UID      UI: 1.3.6.1.4.1.5962.1.1.4.1.1.20040826185059.5457
    (0002,0010) Transfer Syntax UID                 UI: Explicit VR Little Endian
    (0002,0012) Implementation Class UID            UI: 1.3.6.1.4.1.5962.2
    (0002,0013) Implementation Version Name         SH: 'DCTOOL100'
    (0002,0016) Source Application Entity Title     AE: 'CLUNIE1'
    -------------------------------------------------
    (0008,0008) Image Type                          CS: ['DERIVED', 'SECONDARY', 'OTHER']
    (0008,0012) Instance Creation Date              DA: '20040826'
    (0008,0013) Instance Creation Time              TM: '185434'
    (0008,0014) Instance Creator UID                UI: 1.3.6.1.4.1.5962.3
    (0008,0016) SOP Class UID                       UI: MR Image Storage
    (0008,0018) SOP Instance UID                    UI: 1.3.6.1.4.1.5962.1.1.4.1.1.20040826185059.5457
    (0008,0020) Study Date                          DA: '20040826'
    (0008,0021) Series Date                         DA: ''
    (0008,0022) Acquisition Date                    DA: ''
    (0008,0030) Study Time                          TM: '185059'
    (0008,0031) Series Time                         TM: ''
    (0008,0032) Acquisition Time                    TM: ''
    (0008,0050) Accession Number                    SH: ''
    (0008,0060) Modality                            CS: 'MR'
    (0008,0070) Manufacturer                        LO: 'TOSHIBA_MEC'
    (0008,0080) Institution Name                    LO: 'TOSHIBA'
    (0008,0090) Referring Physician's Name          PN: ''
    (0008,0201) Timezone Offset From UTC            SH: '-0400'
    (0008,1010) Station Name                        SH: '000000000'
    (0008,1060) Name of Physician(s) Reading Study  PN: '----'
    (0008,1070) Operators' Name                     PN: '----'
    (0008,1090) Manufacturer's Model Name           LO: 'MRT50H1'
    (0010,0010) Patient's Name                      PN: 'CompressedSamples^MR1'
    (0010,0020) Patient ID                          LO: '4MR1'
    (0010,0030) Patient's Birth Date                DA: ''
    (0010,0040) Patient's Sex                       CS: 'F'
    (0010,1020) Patient's Size                      DS: None
    (0010,1030) Patient's Weight                    DS: '80.0000'
    (0018,0010) Contrast/Bolus Agent                LO: ''
    (0018,0020) Scanning Sequence                   CS: 'SE'
    (0018,0021) Sequence Variant                    CS: 'NONE'
    (0018,0022) Scan Options                        CS: ''
    (0018,0023) MR Acquisition Type                 CS: '3D'
    (0018,0050) Slice Thickness                     DS: '0.8000'
    (0018,0080) Repetition Time                     DS: '4000.0000'
    (0018,0081) Echo Time                           DS: '240.0000'
    (0018,0083) Number of Averages                  DS: '1.0000'
    (0018,0084) Imaging Frequency                   DS: '63.92433900'
    (0018,0085) Imaged Nucleus                      SH: 'H'
    (0018,0086) Echo Number(s)                      IS: '1'
    (0018,0091) Echo Train Length                   IS: None
    (0018,1000) Device Serial Number                LO: '-0000200'
    (0018,1020) Software Versions                   LO: 'V3.51*P25'
    (0018,1314) Flip Angle                          DS: '90'
    (0018,5100) Patient Position                    CS: 'HFS'
    (0020,000D) Study Instance UID                  UI: 1.3.6.1.4.1.5962.1.2.4.20040826185059.5457
    (0020,000E) Series Instance UID                 UI: 1.3.6.1.4.1.5962.1.3.4.1.20040826185059.5457
    (0020,0010) Study ID                            SH: '4MR1'
    (0020,0011) Series Number                       IS: '1'
    (0020,0012) Acquisition Number                  IS: '0'
    (0020,0013) Instance Number                     IS: '1'
    (0020,0032) Image Position (Patient)            DS: [-83.9063, -91.2000, 6.6406]
    (0020,0037) Image Orientation (Patient)         DS: [1.0000, 0.0000, 0.0000, 0.0000, 1.0000, 0.0000]
    (0020,0052) Frame of Reference UID              UI: 1.3.6.1.4.1.5962.1.4.4.1.20040826185059.5457
    (0020,0060) Laterality                          CS: ''
    (0020,1040) Position Reference Indicator        LO: ''
    (0020,1041) Slice Location                      DS: '0.0000'
    (0020,4000) Image Comments                      LT: 'Uncompressed'
    (0028,0002) Samples per Pixel                   US: 1
    (0028,0004) Photometric Interpretation          CS: 'MONOCHROME2'
    (0028,0010) Rows                                US: 8
    (0028,0011) Columns                             US: 8
    (0028,0030) Pixel Spacing                       DS: [0.3125, 0.3125]
    (0028,0100) Bits Allocated                      US: 16
    (0028,0101) Bits Stored                         US: 16
    (0028,0102) High Bit                            US: 15
    (0028,0103) Pixel Representation                US: 1
    (0028,0106) Smallest Image Pixel Value          SS: 0
    (0028,0107) Largest Image Pixel Value           SS: 4000
    (0028,1050) Window Center                       DS: '600'
    (0028,1051) Window Width                        DS: '1600'
    (7FE0,0010) Pixel Data                          OW: Array of 128 elements
    (FFFC,FFFC) Data Set Trailing Padding           OB: Array of 126 elements






|

.. code-block:: Python


    # authors : Guillaume Lemaitre <g.lemaitre58@gmail.com>
    # license : MIT

    from pydicom import examples

    print(__doc__)

    # FIXME: add a full-sized MR image in the testing data
    ds = examples.mr

    # get the pixel information into a numpy array
    arr = ds.pixel_array
    print(f"The image has {arr.shape[0]} x {arr.shape[1]} voxels")
    arr_downsampled = arr[::8, ::8]
    print(
        f"The downsampled image has {arr_downsampled.shape[0]} x {arr_downsampled.shape[1]} voxels"
    )

    # copy the data back to the original data set
    ds.PixelData = arr_downsampled.tobytes()
    # update the information regarding the shape of the data array
    ds.Rows, ds.Columns = arr_downsampled.shape

    # print the image information given in the dataset
    print("The information of the data set after downsampling: \n")
    print(ds)


.. _sphx_glr_download_auto_examples_image_processing_plot_downsize_image.py:

.. only:: html

  .. container:: sphx-glr-footer sphx-glr-footer-example

    .. container:: sphx-glr-download sphx-glr-download-jupyter

      :download:`Download Jupyter notebook: plot_downsize_image.ipynb <plot_downsize_image.ipynb>`

    .. container:: sphx-glr-download sphx-glr-download-python

      :download:`Download Python source code: plot_downsize_image.py <plot_downsize_image.py>`

    .. container:: sphx-glr-download sphx-glr-download-zip

      :download:`Download zipped: plot_downsize_image.zip <plot_downsize_image.zip>`


.. only:: html

 .. rst-class:: sphx-glr-signature

    `Gallery generated by Sphinx-Gallery <https://sphinx-gallery.github.io>`_
