Workflow to preprocess the tiles for the 2.5D reconstruction

scripts/linum_get_slices_ids.py

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+#!/usr/bin/env python
+# -*- coding: utf-8 -*-
+
+"""List the slice ids from a tiles directory"""
+
+import argparse
+import csv
+from pathlib import Path
+import numpy as np
+
+from linumpy.reconstruction import get_tiles_ids
+
+
+def _build_arg_parser():
+    p = argparse.ArgumentParser(
+        description=__doc__, formatter_class=argparse.RawTextHelpFormatter)
+    p.add_argument("directory",
+                   help="Tiles directory")
+    p.add_argument("output_file",
+                   help="Output CSV file")
+    return p
+
+
+def main():
+    # Parse arguments
+    p = _build_arg_parser()
+    args = p.parse_args()
+
+    # Extract the parameters
+    tiles_directory = Path(args.directory)
+    output_file = Path(args.output_file)
+    assert output_file.name.endswith(".csv"), "The output file must be as csv file"
+
+    # Detect the tiles
+    tiles, tiles_ids = get_tiles_ids(tiles_directory)
+
+    # Extract the list of slice ids
+    z_list = []
+    for id in tiles_ids:
+        z_list.append(id[2])
+    z_list = list(set(z_list))
+
+    # Save the ids to a csv file
+    data = np.array([z_list, ]).T
+    with open(output_file, "w") as csv_file:
+        writer = csv.writer(csv_file, delimiter=",")
+        writer.writerow(["slice_id"])
+        writer.writerows(data)
+
+
+if __name__ == "__main__":
+    main()

workflows/workflow_2.5d_preprocessing.nf

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+#!/usr/bin/env nextflow
+nextflow.enable.dsl=2
+
+/* S-OCT 2.5D Preprocessing */
+/* This workflow will generate the mosaic grids and compute the XY shifts between slices
+
+To execute this script, you can use the following command (example):
+
+nextflow run workflow_2.5d_preprocessing.nf --directory <PATH_TO_DATADIR> --output_directory . -resume
+
+Notes
+-----
+Copy this workflow in the processing directory.
+Add the -resume flag to resume the pipeline from the last successfully completed process.
+*/
+
+// Parameters
+params.directory = ""
+params.tiles_directory = params.directory + "/tiles"
+params.output_directory = params.directory
+params.mosaicgrids_directory = params.output_directory + "/mosaic_grids_2d"
+
+/* Processes */
+// Compute the shift between the slices
+process compute_xy_shifts{
+    input:
+        path directory
+    output:
+        path "shifts_xy.csv"
+    publishDir path: "${params.output_directory}", mode: "copy"
+    script:
+        """
+        linum_estimate_xyShift_fromMetadata $directory shifts_xy.csv
+        """
+}
+
+// Detect the slices to process
+process detect_slices{
+    input:
+        path directory
+    output:
+        path "slice_ids.csv"
+    script:
+        """
+        linum_get_slices_ids $directory slice_ids.csv
+        """
+}
+
+// Create the 2D mosaic grid
+process create_mosaicgrid_2d{
+    input:
+        path(directory)
+        val(slice_id)
+    output:
+        path "*.tiff"
+    maxForks 1
+    publishDir path: "${params.mosaicgrids_directory}", mode: "copy"
+    script:
+    """
+    linum_create_mosaic_grid $directory "mosaic_grid_z${slice_id}.tiff" -z $slice_id --normalize --n_cpus 1
+    """
+}
+
+workflow{
+    // Estimate the shifts between slices
+    compute_xy_shifts(params.tiles_directory)
+
+    // Detect the slices to process
+    detect_slices(params.tiles_directory)
+
+    // Split the slice ids
+    slice_ids = detect_slices.out.splitCsv(header: false, skip: 1).map{it->it[0]}
+
+    // Create all the mosaic grids
+    create_mosaicgrid_2d(params.tiles_directory, slice_ids)
+}
+