lipase/preprocessing.py

"""preprocessing of synchrotron images based on telemosToolbox."""

from ij import IJ
from ij.plugin import ImageCalculator
from catalog import ImageCatalog, Sequence


def compute_max(images_file_path):
    """Computes for each pixel position the maximum at this position in all input images.

    :param list(str) images_file_path:
    :rtype ImagePlus:
    """
    assert len(images_file_path) > 1
    max_image = IJ.openImage(images_file_path[0])
    print('max_image', max_image)

    for image_file_path in images_file_path[2:-1]:
        other_image = IJ.openImage(image_file_path)
        print('other_image', other_image)
        ic = ImageCalculator()
        ic.run("max", max_image, other_image)
    print('max_image', max_image)
    return max_image


def replace_outer_frame(image, band_width):
    """Overwrites the outer band of the image by duplicating the value of the pixels that touch this outer band

    :param ImagePlus image:
    :param int band_width: width of the outer band, in pixels
    :rtype ImagePlus:

    adaptation for the following code from matlab telemosToolbx's estimatedwhiteFluoImageTelemos function
        outer = white_estimate;
        white_estimate = white_estimate(4:(end-3),4:(end-3));
        outer(1:3,4:(end-3))=repmat(white_estimate(1,:),3,1);  # top
        outer((end-2):end,4:(end-3))=repmat(white_estimate(end,:),3,1); # bottom
        outer(:,1:3)=repmat(outer(:,4),1,3); # left
        outer(:,(end-2):end)=repmat(outer(:,end-3),1,3); # right
        white_estimate = outer;
        clear outer;
    """
    raise NotImplementedError()
    return image



def estimate_white(sequences, channel_ids, dark=None):
    """Estimation of the white fluorescence image shape of synchrotron light from experimental images of Telemos microscope.

    :param list(Sequence) sequences:
    :param list(str) channel_ids:
    :param ImagePlus or None dark:
    :rtype ImagePlus:
    Code adapted from matlab telemosToolbx's estimatedwhiteFluoImageTelemos function

    % this function is specific of Telemos images (DISCO line SOLEIL)
        % acquired using micromanager software linked to imageJ

    %% input

    %  nothing : interactive function

    %% output

    %  nothing : the final reference fluorescence image is saved on disk

    %% principe
    %  NB: MICROMANAGER save images in a structured file folder architecture :
    %
    % root folder : name given by the user
    %
    %   subfolders roi(n)_tile1 : n folders for each selected roi
    %           or pos(n) : n folders for each selected position
    %
    %   display_and_comments.txt : file describing the channels acquired
    %
    % in each subfolder roi(n)_tile1 or Pos(n) :
    %       images files with name img_00000000(n)_DM300_327-353_00(p).tif
    %               n = number of time
    %               p = z focal plane
    %               DM300_327-353 = name of the channel
    %       metadata.txt : files describing all metadata associated with the
    %       acquisition : x, y, z position, camera settings .... etc.
    %
    % (Nb: depending on the date of acquisition, an extension fluo is found or
    % not in the name of fluorescence image. This extension is given in
    % contrast to the visible image.)
    %
    % IMAGES : fluorescence images are considered
    %
    %
    % IMPORTANT:
    %       it is expected that in the folders at least several images cover the whole field of view
    %       illuminated by the synchrtron light
    %       IF IT IS NOT THE CASE, IT WON'T WORK
    %
    % BASIC: the estimated white image is the MAX of the selected images
    %       when interactive mode is selected, only first time and first z are
    %       proposed
    %       for automatic computing, all images are taken into account
    %
    % WHAT IS DONE:
    %        0 - the user chosse the channels that are considered  in the estimation of the
    % white fluorescence image
    %
    %       1 - spurious pixels (three lines and columns around the image) are not taken
    % in filtering and replaced by line and column number 4 and end-3
    %
    %       2 - Filtering
    % the estimated dark image is filtered :
    %        opening to remove  white regions brighter than the low frequency signal that should correspond to  synchrotron light shape (should be small)
    %        closing to remove black regions that remains (should be small to avoid synchrotron light shape deformation)
    %        average filtering

    % the image computed should be used  to
    %   - to find the best white z plane from the reference white stack
    %   acquired for ex. using the so called "Matthieu lame"%
    %   - correct images for intensities

    %% use
    %       estimatedwhiteFluoImageTelemos

    %% Comments
    %   adapted from proposals 20161050 and 20171187


    %% Author
    % MF Devaux
    % INRA BIA
    % PVPP

    %% date
    % 5 octobre 2017:
    % 23 mars 2018
    % 3 septembre 2018 : comments and general case
    % 16 avril 2019: name of function and default filtering values
    % 29 avril 2019 : new comments and spurious pixels
    % 27 mai 2019 : offset dark
    %     4 juin 2019 : replace exist by isfolder or isfile
    % 14 juin : close figure at the end
    """
    images_file_path = []
    for sequence in sequences:
        for channel_id in channel_ids:
            channel_index = sequence.get_channel_index(channel_id)
            for frame_index in range(sequence.num_frames):
                for z_index in range(sequence.num_slices):
                    images_file_path.append(sequence.get_image_file_path(channel_index, frame_index, z_index))

    white_estimate = compute_max(images_file_path)
    
    # modifiy spurious pixels on the side of the images
    try:
        replace_outer_frame(white_estimate, 3)
    except NotImplementedError as error:
        print('warning: replace_outer_frame is not implemented yet')

    
    return white_estimate


def find_white_reference_image(white_estimate, white_z_stack):
    """Find the white reference Image among a z stack of reference image the most correlated to the white image estimated from a serie of acquisition.

    :param Image white_estimate:
    :param Sequence white_z_stack:
    % this function is specific of Telemos images (DISCO line SOLEIL)
        % acquired using micromanager software linked to imageJ

    %% input
    %  nothing : interactive function

    %% output
    %    zmax : focal plane

    %% principe
    % images were acquired for a given roi which position is found in
    % metadata.txt file
    % white and dark  images were recorded for the full field of view of the DISCO
    % TELEMOS camera
    %
    % correlation between a estimated  white fluorescence image estalished from
    % actual acquisitions of a given sample and all z plane acquired for the reference TELEMOS white
    % image (Matthieu slide or any fluorescent homogeneous image) :

    % The  estimated  white fluorescence image  is generallly obtained bt using function whiteFluoImageTelemosestimation
    % This is not compulsary as any homogenous sample image hat can roughly show the shape of illumination can be used to find
    % the white reference image
    %
    %
    % the z plane for which the maximum correlation is observed between estimated white and reference white images is retained.
    % the white image is then offsetted (its corresponding Dark is subtracted) and copied in the subfolder <WhiteReference> of the sample
    % rootfolder to show that it has been specifically selected for the considered experiment
    %The matlab corrcoeff function is used
    %
    % correlation coefficients are saved in a file called
    % 'corr.txt' in the subfolder 'WhiteReference'
    %
    %
    % expected input folder hierarchy:
    %
    %      >sampleFolder
    %           > PosFolders or RoiFolders
    %           > WhiteEstimate
    %       >darkFolder
    %       >darkFolder.smooth
    %       >whiteFolder
    %           > darkFolderforWhite
    %           > darkFolderforWhite.smooth
    %       >whiteFolder.smooth
    %
    %
    % expected output folder hierarchy:
    %
    %      >sampleFolder
    %           > PosFolders or RoiFolders
    %           > WhiteEstimate
    %           > WhiteReference
    %                   > white after offset
    %       >darkFolder
    %       >darkFolder.smooth
    %       >whiteFolder
    %           > darkFolderforWhite
    %           > darkFolderforWhite.smooth
    %       >whiteFolder.smooth





    %% use
    % [zmax]=findWhiteReferenceImageTelemos

    %% Comments
    %   written for  proposal 20161050
    %   adapted for proposal 20170043


    %% Author
    % MF Devaux
    % INRA BIA
    % PVPP

    %% date
    % 5 octobre 2017:
    % 15 decembre 2017 : adapted to take into account the roi known from
    % metadata
    % 27 fevrier 2018 : comments details
    % 4 septembre 2018: comments and check and naming of folders
    % 12 mars 2019 : save white reference with the same size as white estimate
    % 16 avril 2019 : include diagonals to check the relevance of white
    % reference
    % 20 mai 2019 : track folder
    % 27 mai 2019 : offset dark
    %     4 juin 2019 : replace exist by isfolder or isfile
    """
    raise NotImplementedError()


def test_preprocessing():
    """Test preprocessing."""
    catalog = ImageCatalog('/Users/graffy/ownCloud/ipr/lipase/raw-images')
    sequence = catalog.sequences['res_soleil2018/GGH/GGH_2018_cin2_phiG_I_327_vis_-40_1/Pos2']
    white_estimate = estimate_white([sequence], ['DM300_327-353_fluo'])
    find_white_reference_image(white_estimate, sequence.get_white())


if __name__ == '__main__':
    test_preprocessing()