Difference between revisions of "IJ2-python-lib"

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== Documentation ==
 
== Documentation ==
  
The best documentation is [https://github.com/hadim/ij2-python-lib/tree/master/src/main/resources/ij2_tools the source code] but I'll give some usage examples here.   
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The best documentation is [https://github.com/hadim/ij2-python-lib/tree/master/src/main/resources/ij2_tools the source code].
 +
 
 +
Some functions have <code>ij</code> has a first argument, it excepts to receive an <code>ImageJ</code> object.   
 +
 
 +
<source lang="python"># Do a maximum Z projection
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from ij2_tools.z_projection import do_z_projection
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do_z_projection(ij, data, save=False, output_dir="")
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# Apply a DOG filter
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from ij2_tools.dog_filtering import apply_dog_filter
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apply_dog_filter(ij, data, sigma1, sigma2, save=False, output_dir="")
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# Apply automatic threshold on an image
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# Method is string representing available algorithm in `ops.threshold`
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from ij2_tools.threshold import do_threshold
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do_threshold(ij, data, method, k1=1, save=False, output_dir="")
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# Subtract the first image of a stack to the entire stack
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from ij2_tools.subtract import subtract_first_image
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subtract_first_image(ij, data, save=False, output_dir=""):
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 +
# Print dataset dimensions for X, Y, Z, TIME and CHANNEL
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from ij2_tools.ij_utils import print_info
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# Check if a point is inside a circle
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from ij2_tools.geometry import in_circle
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in_circle(point, center, radius)
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# Return the points defining a circle
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from ij2_tools.geometry import get_circle_points
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get_circle_points(x_center, y_center, radius, n=20)
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# Return the points defining the association of two circles
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from ij2_tools.geometry import get_two_circles_points
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get_two_circles_points(x1, y1, x2, y2, radius, n=20)
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 +
# Detect spots using the TrackMate DOG Detector
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from ij2_tools.spot_detector import dog_detector
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dog_detector(ij, data, radius, relative_threshold=1, doSubpixel=True, doMedian=False, calibration=None)
 +
 
 +
# Return the IJ1 ROI Manager
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from ij2_tools.ij1 import get_roi_manager
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get_roi_manager(new=False)</source>
  
 
== Related links ==
 
== Related links ==

Revision as of 17:57, 15 November 2016

ij2-python-lib (Fiji)
Author Hadrien Mary
Maintainer Hadrien Mary
Source on GitHub
Initial release 15/11/2016
Development status v0.1.0, development


Presentation

ij2-python-lib is a set of IJ2 Python Libraries.

Note that this library has been designed to regroup useful functions the author use often. And so many functions are very specific to the use-case of the author.

Install

Add the Hadim update site in Help ▶ Update… (see http://imagej.net/Following_an_update_site for details on how to proceed).

Documentation

The best documentation is the source code.

Some functions have ij has a first argument, it excepts to receive an ImageJ object.

# Do a maximum Z projection
from ij2_tools.z_projection import do_z_projection
do_z_projection(ij, data, save=False, output_dir="")

# Apply a DOG filter
from ij2_tools.dog_filtering import apply_dog_filter
apply_dog_filter(ij, data, sigma1, sigma2, save=False, output_dir="")

# Apply automatic threshold on an image
# Method is string representing available algorithm in `ops.threshold`
from ij2_tools.threshold import do_threshold
do_threshold(ij, data, method, k1=1, save=False, output_dir="")

# Subtract the first image of a stack to the entire stack
from ij2_tools.subtract import subtract_first_image
subtract_first_image(ij, data, save=False, output_dir=""):

# Print dataset dimensions for X, Y, Z, TIME and CHANNEL
from ij2_tools.ij_utils import print_info

# Check if a point is inside a circle
from ij2_tools.geometry import in_circle
in_circle(point, center, radius)

# Return the points defining a circle
from ij2_tools.geometry import get_circle_points
get_circle_points(x_center, y_center, radius, n=20)

# Return the points defining the association of two circles
from ij2_tools.geometry import get_two_circles_points
get_two_circles_points(x1, y1, x2, y2, radius, n=20)

# Detect spots using the TrackMate DOG Detector
from ij2_tools.spot_detector import dog_detector
dog_detector(ij, data, radius, relative_threshold=1, doSubpixel=True, doMedian=False, calibration=None)

# Return the IJ1 ROI Manager
from ij2_tools.ij1 import get_roi_manager
get_roi_manager(new=False)

Related links

Authors

ij2-python-lib has been created by Hadrien Mary.

This work started in 2016 at the Gary Brouhard laboratory (http://brouhardlab.mcgill.ca) at McGill University.