--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/basic_illumination.xml	Fri Mar 12 00:13:46 2021 +0000
@@ -0,0 +1,50 @@
+<tool id="basic_illumination" name="BaSiC Illumination" version="@VERSION@.3" profile="17.09">
+    <description>ImageJ BaSiC shading correction for use with Ashlar</description>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+ 
+    <expand macro="requirements"/>
+    @VERSION_CMD@
+
+    <command detect_errors="exit_code"><![CDATA[
+    ln -s $in_files "${in_files.name}" &&
+
+    #set $outname = str($in_files.name).replace('.ome.tiff','')
+
+    @CMD_BEGIN@
+
+    "filename='${in_files.name}',output_dir='.',experiment_name='output'";
+
+    ]]></command>
+
+    <inputs>
+        <param type="data" name="in_files" format="tiff" label="Raw Cycle Images"/>
+   </inputs>
+
+   <outputs>
+       <data format="tiff" name="output_dfp" label="${tool.name} on ${on_string}: DFP" from_work_dir="output-dfp.tif"/>
+       <data format="tiff" name="output_ffp" label="${tool.name} on ${on_string}: FFP" from_work_dir="output-ffp.tif"/>
+    </outputs>
+
+    <help><![CDATA[
+basic-illumination
+ImageJ BaSiC shading correction for use with Ashlar
+
+Running as a Docker container
+Create a container:
+
+docker run -it -v /path/to/data:/data labsyspharm/basic-illumination bash
+(where /path/to/data is the data directory on your local machine. Your data will be mapped to /data inside the container)
+
+Once inside the container, do ls /data to ensure your data is there, followed by
+
+ImageJ-linux64 --ij2 --headless --run imagej_basic_ashlar.py \
+  "filename='/data/input.ome.tiff',output_dir='/data/',experiment_name='my_experiment'"
+for each input.ome.tiff in your data directory.
+
+OHSU Wrapper Repo: https://github.com/ohsu-comp-bio/basic-illumination
+Conda Package Available From: https://anaconda.org/ohsu-comp-bio/basic-illumination
+    ]]></help>
+    <expand macro="citations" />
+</tool>

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/imagej_basic_ashlar.py	Fri Mar 12 00:13:46 2021 +0000
@@ -0,0 +1,135 @@
+# @File(label="Select a slide to process") filename
+# @File(label="Select the output location", style="directory") output_dir
+# @String(label="Experiment name (base name for output files)") experiment_name
+# @Float(label="Flat field smoothing parameter (0 for automatic)", value=0.1) lambda_flat
+# @Float(label="Dark field smoothing parameter (0 for automatic)", value=0.01) lambda_dark
+
+# Takes a slide (or other multi-series BioFormats-compatible file set) and
+# generates flat- and dark-field correction profile images with BaSiC. The
+# output format is two multi-series TIFF files (one for flat and one for dark)
+# which is the input format used by Ashlar.
+
+# Invocation for running from the commandline:
+#
+# ImageJ --ij2 --headless --run imagej_basic_ashlar.py "filename='input.ext',output_dir='output',experiment_name='my_experiment'"
+
+import sys
+from ij import IJ, WindowManager, Prefs
+from ij.macro import Interpreter
+from loci.plugins import BF
+from loci.plugins.in import ImporterOptions
+from loci.formats import ImageReader
+from loci.formats.in import DynamicMetadataOptions
+import BaSiC_ as Basic
+
+import pdb
+
+
+def main():
+
+    Interpreter.batchMode = True
+
+    if (lambda_flat == 0) ^ (lambda_dark == 0):
+        print ("ERROR: Both of lambda_flat and lambda_dark must be zero,"
+               " or both non-zero.")
+        return
+    lambda_estimate = "Automatic" if lambda_flat == 0 else "Manual"
+
+    print "Loading images..."
+
+    # For multi-scene .CZI files, we need raw tiles instead of the
+    # auto-stitched mosaic and we don't want labels or overview images.  This
+    # only affects BF.openImagePlus, not direct use of the BioFormats reader
+    # classes which we also do (see below)
+    Prefs.set("bioformats.zeissczi.allow.autostitch",  "false")
+    Prefs.set("bioformats.zeissczi.include.attachments", "false")
+
+    # Use BioFormats reader directly to determine dataset dimensions without
+    # reading every single image. The series count (num_images) is the one value
+    # we can't easily get any other way, but we might as well grab the others
+    # while we have the reader available.
+    dyn_options = DynamicMetadataOptions()
+    # Directly calling a BioFormats reader will not use the IJ Prefs settings
+    # so we need to pass these options explicitly.
+    dyn_options.setBoolean("zeissczi.autostitch", False)
+    dyn_options.setBoolean("zeissczi.attachments", False)
+    bfreader = ImageReader()
+    bfreader.setMetadataOptions(dyn_options)
+    bfreader.id = str(filename)
+    num_images = bfreader.seriesCount
+    num_channels = bfreader.sizeC
+    width = bfreader.sizeX
+    height = bfreader.sizeY
+    bfreader.close()
+
+    # The internal initialization of the BaSiC code fails when we invoke it via
+    # scripting, unless we explicitly set a the private 'noOfSlices' field.
+    # Since it's private, we need to use Java reflection to access it.
+    Basic_noOfSlices = Basic.getDeclaredField('noOfSlices')
+    Basic_noOfSlices.setAccessible(True)
+    basic = Basic()
+    Basic_noOfSlices.setInt(basic, num_images)
+
+    # Pre-allocate the output profile images, since we have all the dimensions.
+    ff_image = IJ.createImage("Flat-field", width, height, num_channels, 32);
+    df_image = IJ.createImage("Dark-field", width, height, num_channels, 32);
+
+    print("\n\n")
+
+    # BaSiC works on one channel at a time, so we only read the images from one
+    # channel at a time to limit memory usage.
+    for channel in range(num_channels):
+        print "Processing channel %d/%d..." % (channel + 1, num_channels)
+        print "==========================="
+
+        options = ImporterOptions()
+        options.id = str(filename)
+        options.setOpenAllSeries(True)
+        # concatenate=True gives us a single stack rather than a list of
+        # separate images.
+        options.setConcatenate(True)
+        # Limit the reader to the channel we're currently working on. This loop
+        # is mainly why we need to know num_images before opening anything.
+        for i in range(num_images):
+            options.setCBegin(i, channel)
+            options.setCEnd(i, channel)
+        # openImagePlus returns a list of images, but we expect just one (a
+        # stack).
+        input_image = BF.openImagePlus(options)[0]
+
+        # BaSiC seems to require the input image is actually the ImageJ
+        # "current" image, otherwise it prints an error and aborts.
+        WindowManager.setTempCurrentImage(input_image)
+        basic.exec(
+            input_image, None, None,
+            "Estimate shading profiles", "Estimate both flat-field and dark-field",
+            lambda_estimate, lambda_flat, lambda_dark,
+            "Ignore", "Compute shading only"
+        )
+        input_image.close()
+
+        # Copy the pixels from the BaSiC-generated profile images to the
+        # corresponding channel of our output images.
+        ff_channel = WindowManager.getImage("Flat-field:%s" % input_image.title)
+        ff_image.slice = channel + 1
+        ff_image.getProcessor().insert(ff_channel.getProcessor(), 0, 0)
+        ff_channel.close()
+        df_channel = WindowManager.getImage("Dark-field:%s" % input_image.title)
+        df_image.slice = channel + 1
+        df_image.getProcessor().insert(df_channel.getProcessor(), 0, 0)
+        df_channel.close()
+
+        print("\n\n")
+
+    template = '%s/%s-%%s.tif' % (output_dir, experiment_name)
+    ff_filename = template % 'ffp'
+    IJ.saveAsTiff(ff_image, ff_filename)
+    ff_image.close()
+    df_filename = template % 'dfp'
+    IJ.saveAsTiff(df_image, df_filename)
+    df_image.close()
+
+    print "Done!"
+
+
+main()

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/imagej_basic_ashlar_filepattern.py	Fri Mar 12 00:13:46 2021 +0000
@@ -0,0 +1,186 @@
+# @String(label="Enter a filename pattern describing the TIFFs to process") pattern
+# @File(label="Select the output location", style="directory") output_dir
+# @String(label="Experiment name (base name for output files)") experiment_name
+# @Float(label="Flat field smoothing parameter (0 for automatic)", value=0.1) lambda_flat
+# @Float(label="Dark field smoothing parameter (0 for automatic)", value=0.01) lambda_dark
+
+# Takes a filename pattern describing a list of image files and generates flat-
+# and dark-field correction profile images with BaSiC. The pattern must contain
+# a "*" wildcard to indicate the part of the filename that varies with the image
+# series number. If the images are stored with one channel per file then the
+# pattern must also contain the placeholder {channel} in place of the channel
+# name or number. If the image files are multi-channel then the {channel}
+# placeholder must be omitted. The output format is two multi-channel TIFF files
+# (one for flat and one for dark) which is the input format used by Ashlar.
+
+# Invocation for running from the commandline:
+# (to match files like "s001_c1.tif", "s001_c2.tif", "s002_c1.tif", etc.)
+#
+# ImageJ --ij2 --headless --run imagej_basic_ashlar_filepattern.py "pattern='input/s*_c{channel}.tif',output_dir='output',experiment_name='my_experiment'"
+
+import sys
+import os
+import re
+import collections
+from ij import IJ, WindowManager, ImagePlus, ImageStack
+from ij.io import Opener
+from ij.macro import Interpreter
+import BaSiC_ as Basic
+
+
+def enumerate_filenames(pattern):
+    """Return filenames matching pattern (a glob pattern containing an optional
+    {channel} placeholder).
+
+    Returns a list of lists, where the top level is indexed by sorted channel
+    name/number and the bottom level is filenames for that channel.
+
+    """
+    (base, pattern) = os.path.split(pattern)
+    regex = re.sub(r'{([^:}]+)(?:[^}]*)}', r'(?P<\1>.*?)',
+                   pattern.replace('.', '\.').replace('*', '.*?'))
+    channels = set()
+    num_images = 0
+    # Dict[Union[int, str, None], List[str]]
+    filenames = collections.defaultdict(list)
+    for f in os.listdir(base):
+        match = re.match(regex, f)
+        if match:
+            gd = match.groupdict()
+            channel = gd.get('channel', None)
+            try:
+                channel = int(channel)
+            except (ValueError, TypeError):
+                pass
+            channels.add(channel)
+            filenames[channel].append(os.path.join(base, f))
+            num_images += 1
+    if num_images % len(channels) != 0:
+        print (
+            "ERROR: Some image files seem to be missing --"
+            " image count (%d) is not a multiple of channel count (%d)"
+            % (num_images, len(channels))
+        )
+        return []
+    channels = sorted(channels)
+    if len(channels) > 1:
+        print("Detected the following channel names/numbers from filenames:")
+        for channel in channels:
+            print("    %s" % channel)
+    filenames = [filenames[channel] for channel in channels]
+    return filenames
+
+
+def main():
+
+    Interpreter.batchMode = True
+
+    if (lambda_flat == 0) ^ (lambda_dark == 0):
+        print ("ERROR: Both of lambda_flat and lambda_dark must be zero,"
+               " or both non-zero.")
+        return
+    lambda_estimate = "Automatic" if lambda_flat == 0 else "Manual"
+
+    print "Loading images..."
+    filenames = enumerate_filenames(pattern)
+    if len(filenames) == 0:
+        return
+    # This is the number of channels inferred from the filenames. The number
+    # of channels in an individual image file will be determined below.
+    num_channels = len(filenames)
+    num_images = len(filenames[0])
+    image = Opener().openImage(filenames[0][0])
+    if image.getNDimensions() > 3:
+        print "ERROR: Can't handle images with more than 3 dimensions."
+    (width, height, channels, slices, frames) = image.getDimensions()
+    # The third dimension could be any of these three, but the other two are
+    # guaranteed to be equal to 1 since we know NDimensions is <= 3.
+    image_channels = max((channels, slices, frames))
+    image.close()
+    if num_channels > 1 and image_channels > 1:
+        print (
+            "ERROR: Can only handle single-channel images with {channel} in"
+            " the pattern, or multi-channel images without {channel}. The"
+            " filename patterns imply %d channels and the images themselves"
+            " have %d channels." % (num_channels, image_channels)
+        )
+        return
+    if image_channels == 1:
+        multi_channel = False
+    else:
+        print (
+            "Detected multi-channel image files with %d channels"
+            % image_channels
+        )
+        multi_channel = True
+        num_channels = image_channels
+        # Clone the filename list across all channels. We will handle reading
+        # the individual image planes for each channel below.
+        filenames = filenames * num_channels
+
+    # The internal initialization of the BaSiC code fails when we invoke it via
+    # scripting, unless we explicitly set a the private 'noOfSlices' field.
+    # Since it's private, we need to use Java reflection to access it.
+    Basic_noOfSlices = Basic.getDeclaredField('noOfSlices')
+    Basic_noOfSlices.setAccessible(True)
+    basic = Basic()
+    Basic_noOfSlices.setInt(basic, num_images)
+
+    # Pre-allocate the output profile images, since we have all the dimensions.
+    ff_image = IJ.createImage("Flat-field", width, height, num_channels, 32);
+    df_image = IJ.createImage("Dark-field", width, height, num_channels, 32);
+
+    print("\n\n")
+
+    # BaSiC works on one channel at a time, so we only read the images from one
+    # channel at a time to limit memory usage.
+    for channel in range(num_channels):
+        print "Processing channel %d/%d..." % (channel + 1, num_channels)
+        print "==========================="
+
+        stack = ImageStack(width, height, num_images)
+        opener = Opener()
+        for i, filename in enumerate(filenames[channel]):
+            print "Loading image %d/%d" % (i + 1, num_images)
+            # For multi-channel images the channel determines the plane to read.
+            args = [channel + 1] if multi_channel else []
+            image = opener.openImage(filename, *args)
+            stack.setProcessor(image.getProcessor(), i + 1)
+        input_image = ImagePlus("input", stack)
+
+        # BaSiC seems to require the input image is actually the ImageJ
+        # "current" image, otherwise it prints an error and aborts.
+        WindowManager.setTempCurrentImage(input_image)
+        basic.exec(
+            input_image, None, None,
+            "Estimate shading profiles", "Estimate both flat-field and dark-field",
+            lambda_estimate, lambda_flat, lambda_dark,
+            "Ignore", "Compute shading only"
+        )
+        input_image.close()
+
+        # Copy the pixels from the BaSiC-generated profile images to the
+        # corresponding channel of our output images.
+        ff_channel = WindowManager.getImage("Flat-field:%s" % input_image.title)
+        ff_image.slice = channel + 1
+        ff_image.getProcessor().insert(ff_channel.getProcessor(), 0, 0)
+        ff_channel.close()
+        df_channel = WindowManager.getImage("Dark-field:%s" % input_image.title)
+        df_image.slice = channel + 1
+        df_image.getProcessor().insert(df_channel.getProcessor(), 0, 0)
+        df_channel.close()
+
+        print("\n\n")
+
+    template = '%s/%s-%%s.tif' % (output_dir, experiment_name)
+    ff_filename = template % 'ffp'
+    IJ.saveAsTiff(ff_image, ff_filename)
+    ff_image.close()
+    df_filename = template % 'dfp'
+    IJ.saveAsTiff(df_image, df_filename)
+    df_image.close()
+
+    print "Done!"
+
+
+main()

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/macros.xml	Fri Mar 12 00:13:46 2021 +0000
@@ -0,0 +1,20 @@
+<?xml version="1.0"?>
+<macros>
+    <xml name="requirements">
+        <requirements>
+            <requirement type="package" version="3.8">python</requirement>
+            <requirement type="package" version="1.0.2">basic-illumination</requirement>
+        </requirements>
+    </xml>
+
+    <xml name="version_cmd">
+        <version_command>echo @VERSION@</version_command>
+    </xml>
+    <xml name="citations">
+        <citations>
+        </citations>
+    </xml>
+
+    <token name="@VERSION@">1.0.2</token>
+    <token name="@CMD_BEGIN@">ImageJ --ij2 --headless --run ${__tool_directory__}/imagej_basic_ashlar.py</token>
+</macros>