Metadata-Version: 1.0
Name: FluorSeg
Version: 0.0.24dev
Summary: Segment regions from fluorescence images
Home-page: https://github.com/TeamMacLean/fluorseg
Author: Dan MacLean
Author-email: dan.maclean@tsl.ac.uk
License: LICENSE.txt
Description: ===========
        FluorSeg
        ===========
        
        FlourSeg provides such and such and so and so. You might find
        it most useful for tasks involving <x> and also <y>. Typical usage
        often looks like this::
        
            #!/usr/bin/env python
        
            from fluorseg import liffile
            from fluorseg import roifile
        
            lif = liffile.LIFFile(path)
        
            #show the path
            print(lif.path)
        
            #show the metadata xml object
            print(lif.xml_root)
        
            #show the number of images in the file
            print(lif.img_count)
        
            #show the number of layers in each zstack for each image
            print(lif.z_stack_count)
        
            #show the first image's, 2nd zstack layer
            print(type(lif.combined_channel_images[0][1]))
        
            #show the type first channel of the first image's 2nd z-stack layer - each data array is a numpy ndarray
            # they are held in nested lists => [image index][z_stack index]
            print(type(lif.channel_one_images[0][1]))
        
            #plot the second channel of the first image's 1st z-stack layer [image index][z_stack index]
            plt.imshow(lif.channel_two_images[0][0], interpolation='nearest')
            plt.show()
        
            #get the maximum projection of each images z-stack for each image
            max_projs_channel_one = [liffile.max_proj(z_stacks) for z_stacks in lif.channel_one_images]
            max_projs_channel_two = [liffile.max_proj(z_stacks) for z_stacks in lif.channel_two_images]
        
            #plot the first max_proj
            plt.imshow(max_projs_channel_one[0], interpolation='nearest')
            plt.show()
        
            plt.imshow(max_projs_channel_two[0], interpolation='nearest')
            plt.show()
        
            #get the region of interest info
            roi_info = roifile.ROIFile(roi_zip_path) #roi for series 001 only
        
            #make the mask for the second region of interest - a polygon
            mask = make_polygon_mask(roi_info.rois[1], 512, 512)
        
            #make the mask for the 5th region of interest - an ellipse
            oval_mask = make_oval_mask(roi_info.rois[4], 512,512)
        
            #just get the volume in a region of interest - masking done for you
            series1_mp_c2 = max_projs_channel_two[0]
            get_region_volume(series1_mp_c2, roi_info.rois[4])
        
        
        
        (Note the double-colon and 4-space indent formatting above.)
        
        Paragraphs are separated by blank lines. *Italics*, **bold**,
        and ``monospace`` look like this.
        
        
        A Section
        =========
        
        Lists look like this:
        
        * First
        
        * Second. Can be multiple lines
          but must be indented properly.
        
        A Sub-Section
        -------------
        
        Numbered lists look like you'd expect:
        
        1. hi there
        
        2. must be going
        
        Urls are http://like.this and links can be
        written `like this <http://www.example.com/foo/bar>`_.
Platform: UNKNOWN
