Chunk - {{ chunk_num }} Channel - {{ loop.index0 }}
+Corrected
+Slice-{{ image.slice }}
+Uncorrected
+Slice-{{ image.slice }}
++ Flatfield Correction QC
+ Whole Slice QC +
+ Volume Rendered Image + + \ No newline at end of file diff --git a/qc/resources/volViewer/cm_gray.png b/qc/resources/volViewer/cm_gray.png new file mode 100644 index 0000000..8ac3388 Binary files /dev/null and b/qc/resources/volViewer/cm_gray.png differ diff --git a/qc/resources/volViewer/cm_viridis.png b/qc/resources/volViewer/cm_viridis.png new file mode 100644 index 0000000..80df96b Binary files /dev/null and b/qc/resources/volViewer/cm_viridis.png differ diff --git a/qc/resources/volViewer/volRender.html b/qc/resources/volViewer/volRender.html new file mode 100644 index 0000000..1976f66 --- /dev/null +++ b/qc/resources/volViewer/volRender.html @@ -0,0 +1,22 @@ + + + +
+ Channel {{ loop.index0 }}+ |
+ ||||
|
+ slice - {{ slice.slice }} + |
+ {%- endfor %}
+ ||||
' + +# if not first sample just add the one link +if(path.exists(total_html)): + with open(total_html,'a') as f: + f.write(sub_link) + +# if it is the first sample write out the template +else: + template = env.get_template("qc/resources/qc_report_temp.html") + output = template.render() + output+=sub_link + with open(total_html, 'w') as f: + f.write(output) diff --git a/workflow/scripts/generate_volume_qc.py b/workflow/scripts/generate_volume_qc.py new file mode 100644 index 0000000..5e0c69a --- /dev/null +++ b/workflow/scripts/generate_volume_qc.py @@ -0,0 +1,38 @@ +import json +import shutil +from pathlib import Path +from distutils.dir_util import copy_tree +from zarrnii import ZarrNii +import math + +# directory containing the volume rendering files +resource_dir = Path(snakemake.output.resources) +# where html file should be written +html_dest = snakemake.output.html + +# inputted ome-zarr path +ome_data = snakemake.input.ome + +# move volume renderer into the subjects directory +copy_tree("qc/resources/volViewer", str(resource_dir)) +shutil.move(resource_dir / "volRender.html", html_dest) + +# Get most downsampled ome-zarr image +ds_z = ZarrNii.from_path(ome_data,level=5, channels=[0,1]) +z_length = ds_z.darr.shape[1] + +# downsample it so it has at most 100 slices and ast least 50 slices in z-direction +if(z_length>50): + downsample_factor = math.floor(z_length/50) +else: + downsample_factor = 1 +ds_z = ds_z.downsample(along_z=downsample_factor) + +# Write it to a JSON for js script to read +with open(resource_dir / "volumeData.json", 'w') as f: + json_data = json.dumps(ds_z.darr.compute().tolist()) + f.write(json_data) + + + + diff --git a/workflow/scripts/generate_whole_slice_qc.py b/workflow/scripts/generate_whole_slice_qc.py new file mode 100644 index 0000000..5967b98 --- /dev/null +++ b/workflow/scripts/generate_whole_slice_qc.py @@ -0,0 +1,65 @@ +import os +import math +from ome_zarr.io import parse_url +from ome_zarr.reader import Reader +import matplotlib.pyplot as plt +import numpy as np +from jinja2 import Environment, FileSystemLoader + +# load jinja html template +file_loader = FileSystemLoader(".") +env = Environment(loader=file_loader) +template = env.get_template("qc/resources/ws_html_temp.html") + +# user set configurations +ws_s_step=snakemake.params.ws_s_step +ws_s_start=snakemake.params.ws_s_start +ws_cmap=snakemake.params.ws_cmap + +# input ome-zarr file +ome= snakemake.input.ome + +# output paths +image_dir = snakemake.output.images_dir +out_html = snakemake.output.html + +# read ome-zarr data and convert to list +proc_reader= Reader(parse_url(ome)) +proc_data=list(proc_reader())[0].data + +os.makedirs(image_dir, exist_ok=True) + +channels = [] +# for each channel add the images of the most downsampled data +for chan_num, channel in enumerate(proc_data[-1]): + slice = ws_s_start + chan = [] + slices = [] + while(slice