PyDIP User Manual

Contents

Currently, most functionality in the PyDIP module is directly mirrored from the DIPlib library. That is, function names and signatures are mostly identical to those in DIPlib. Please see the documentation for DIPlib to learn how to use these functions. Type \m_class{m-label m-warning} t here to bring up a search dialog box where you can find functions by name.

To install the package from PyPI, use

pip install diplib

To read images through the Bio-Formats library, you will need to download it separately:

python -m diplib download_bioformats

This user manual discusses the differences with the DIPlib library.

Type correspondences

Most classes defined in DIPlib and used as input arguments to functions have a Python binding, with the following exceptions:

  • dip::DataType: pass a string such as 'UINT8' or 'SFLOAT'.

  • dip::Sample: pass a scalar (a regular Python number).

  • dip::Pixel: pass a list of scalars.

  • dip::Range: pass a slice (slice(0, 3, 1)). Note that the second argument, the end value, is interpreted differently by DIPlib: it is included in the range. You can also pass a scalar here.

  • dip::UnsignedArray, dip::FloatArray, or similar: pass a Python list: [5, 5]. A scalar is accepted as a one-element list.

  • dip::StringArray: pass a list of strings (['foo','bar']).

  • dip::StringSet: pass a dictionary ({'foo','bar'}).

By using named arguments, it is quite simple to set only needed arguments, and leave all others with their default values. All arguments that have a default value in C++ also have a default value in Python.

Displaying images

The class dip.Image has a method Show(). There is an identical function dip.Show(). They display an image to the current matplotlib window, if matplotlib is installed:

import diplib as dip
img = dip.ImageReadTIFF('cameraman')
img.Show()

By default, the image intensities are mapped to the full display range (i.e. the minimum image intensity is black and the maximum is white). This can be changed for example as follows:

img.Show('unit')  # maps [0,1] to the display range
img.Show('8bit')  # maps [0,255] to the display range
img.Show('orientation')  # maps [0,pi] to the display range
img.Show('base')  # keeps 0 to the middle grey level, and uses a divergent color map
img.Show('log')  # uses logarithmic mapping

Type help(dip.Show) in Python to learn about many more options.

If DIPviewer is installed, its functionality will be in the diplib.viewer namespace. Use dip.viewer.Show(img). Depending on the backend used, it will be necessary to do dip.viewer.Spin() to interact with the created window. Spin() interrupts the interactive session until all DIPviewer windows have been closed. Even when Spin() is not needed to interact with the windows, it should be run before closing the Python session to avoid a series of error messages. Alternatively, periodically call dip.viewer.Draw(). dip.viewer.Show() has additional parameters that can be used to set viewing options; type help(dip.viewer.Show) for details. It also returns an object that can be used for further interaction.

Indexing into images

Indexing into a dip.Image object works as it does for other array types in Python:

img[0]
img[0:10]
img[0:-1:2, 0:-1:2]

Note that dimensions are ordered in reverse from how NumPy stores them (the first dimension is horizontal, or x).

It is possible to assign to a subset of the image pixels using indexing:

img[0] = 0
img[0:10] = img[20:30]
img[0:-1:2, 0:-1:2] = 255

Unlike in DIPlib, the square brackets index into spatial dimensions. To index into tensor dimensions, use round brackets (parenthesis):

img(0)
img(0, 2)
img(slice(0, 3))

The output of any of these indexing operations shares data with the original image, so writing to that output also changes the original image:

img2 = img(0)        # this copy shares data with img
img2.Fill(100)       # same as img(0).Fill(100)
img(1).Copy(img(0))
img(2)[:,:] = img(0)

img2 = img(0).Copy() # this copy does not share data with img
img2.Fill(100)       # does not affect img

Irregular indexing using a mask image is also supported. This indexing returns a copy of the data, but an assignment form is also available:

img2 = img[mask]  # this copy does not share data with img
img2.Fill(0)      # does not affect img
img[mask] = 0     # sets all pixels in mask to 0

Testing image validity

Instead of IsForged(), use IsEmpty() to test if an image is forged.

Functions that expect an image interpret None as an empty (non-forged) image.