Add configuration more suitable to DSA.

slicer_cli_plugin/Dockerfile

@@ -10,7 +10,10 @@ RUN pip3 install --upgrade pip
 RUN pip3 install -r /opt/HistoQC/requirements.txt
 RUN pip3 install girder-slicer-cli-web girder-client
 RUN pip3 install large-image[all] --find-links https://girder.github.io/large_image_wheels
+# HistoQC doesn't work with PIL 10
+RUN pip3 install 'Pillow<10'
 
 COPY . $PWD
+RUN cp config_dsa.ini /opt/HistoQC/histoqc/config/.
 
 ENTRYPOINT ["python3", "./cli_list.py"]

slicer_cli_plugin/HistoQC/HistoQC.py

@@ -22,10 +22,15 @@
 girder = girder_client.GirderClient(apiUrl=args.girderApiUrl)
 girder.setToken(args.girderToken)
 
-conf = open('/opt/HistoQC/histoqc/config/config.ini').read()
-conf = conf.replace('confirm_base_mag: False', 'confirm_base_mag: False\nbase_mag: 20')
-conf = open('/opt/HistoQC/histoqc/config/config.ini', 'w').write(conf)
-
+confpath = '/opt/HistoQC/histoqc/config/' + args.config
+if os.path.exists(confpath):
+    conf = open(confpath).read()
+    if '\nbase_mag' not in conf:
+        logging.info('Adding base_mag to %s', confpath)
+        conf = conf.replace('confirm_base_mag: False', 'confirm_base_mag: False\nbase_mag: 20')
+        conf = open(confpath, 'w').write(conf)
+else:
+    confpath = None
 
 input_dir = args.inputDir
 logging.info(f'{input_dir = }')
@@ -97,11 +102,13 @@
 
     os.chdir(histoqc_dir)
 
-    histoqc_output = subprocess.check_output([
+    cmd = [
         "python3", "-m", "histoqc",
         '-o', tmp_output_dir,
         f'{input_dir}/*'
-    ])
+    ] + (['-c', confpath] if confpath else [])
+    logging.info('Running %r', cmd)
+    histoqc_output = subprocess.check_output(cmd)
 
     os.chdir(current_dir)
 

slicer_cli_plugin/HistoQC/HistoQC.xml

@@ -123,7 +123,7 @@
       <longflag>--config</longflag>
       <description><![CDATA[Configuration file to use, defaults to config.ini for H&E images]]></description>
       <label>config</label>
-      <default>config.ini</default>
+      <default>config_dsa.ini</default>
     </string>    
 
   </parameters>

slicer_cli_plugin/config_dsa.ini

@@ -0,0 +1,217 @@
+[pipeline]
+steps= BasicModule.getBasicStats
+    ClassificationModule.byExampleWithFeatures:pen_markings
+    ClassificationModule.byExampleWithFeatures:coverslip_edge
+    LightDarkModule.getIntensityThresholdPercent:tissue
+    LightDarkModule.getIntensityThresholdPercent:darktissue
+    BubbleRegionByRegion.detectSmoothness
+    MorphologyModule.removeFatlikeTissue
+    MorphologyModule.fillSmallHoles
+    MorphologyModule.removeSmallObjects
+    BlurDetectionModule.identifyBlurryRegions
+    BasicModule.finalProcessingSpur
+    BasicModule.finalProcessingArea
+    HistogramModule.compareToTemplates
+    HistogramModule.getHistogram
+    BrightContrastModule.getContrast
+    BrightContrastModule.getBrightnessGray
+    BrightContrastModule.getBrightnessByChannelinColorSpace:RGB
+    BrightContrastModule.getBrightnessByChannelinColorSpace:YUV
+    BrightContrastModule.getContrast:background
+    BrightContrastModule.getBrightnessGray:background
+    BrightContrastModule.getBrightnessByChannelinColorSpace:RGB:background
+    DeconvolutionModule.separateStains
+    SaveModule.saveFinalMask
+    SaveModule.saveMacro
+    SaveModule.saveThumbnails
+    BasicModule.finalComputations
+
+
+[BaseImage.BaseImage]
+image_work_size = 1.25x
+
+#not yet implemented
+confirm_base_mag: False
+base_mag: 20
+
+#three options: relative2mask, absolute, relative2image
+mask_statistics = relative2mask
+
+[BasicModule.getBasicStats]
+image_work_size = 1.25x
+
+#[ClassificationModule.byExample]
+[ClassificationModule.byExampleWithFeatures:pen_markings]
+name: pen_markings
+threshold: .5
+examples: ./pen/1k_version/pen_green.png:./pen/1k_version/pen_green_mask.png
+
+area_threshold: 100
+features:  frangi
+           laplace
+           rgb
+           #lbp
+           #gabor
+           #median
+           #gaussian
+
+laplace_ksize: 3
+
+frangi_scale_range: (1,10)
+frangi_scale_step: 2
+frangi_beta1: .5
+frangi_beta2: 15
+frangi_black_ridges: True
+
+gabor_theta: 4
+gabor_sigma: (1,3)
+gabor_frequency: (0.05, 0.25)
+
+lbp_radius: 3
+lbp_points: 24
+lbp_method: default
+
+median_disk_size: 3
+
+#gaussian_sigma: 1
+#gaussian_multichan: False
+
+
+
+[ClassificationModule.byExampleWithFeatures:coverslip_edge]
+name: coverslip_edge
+threshold: .5
+
+examples: ./models/coverslip_edge_he/coverslip_edge.png:./models/coverslip_edge_he/coverslip_edge_mask.png
+
+area_threshold: 15
+features:  frangi
+           laplace
+           rgb
+
+dilate_kernel_size: 5
+
+[LightDarkModule.getIntensityThresholdPercent:bubble]
+name: bubble
+upper_threshold: .94
+lower_threshold: .82
+upper_variance: 11
+invert: true
+
+
+[LightDarkModule.getIntensityThresholdPercent:tissue]
+name: bright
+upper_threshold: .9
+lower_std: 10
+
+[LightDarkModule.getIntensityThresholdPercent:darktissue]
+name: dark
+upper_threshold: .15
+invert: true
+
+
+[LightDarkModule.getTissuePercent]
+threshold: .8
+
+[LightDarkModule.getDarkTissuePercent]
+threshold: .15
+
+[MorphologyModule.removeSmallObjects]
+min_size: 64
+
+[MorphologyModule.removeFatlikeTissue]
+kernel_size: 10
+max_keep_size: 1000
+fat_cell_size: 64
+
+[MorphologyModule.fillSmallHoles]
+min_size: 1000
+
+[HistogramModule.compareToTemplates]
+limit_to_mask: True
+bins: 20
+templates= ./templates/template1.png
+           ./templates/template2.png
+           ./templates/template3.png
+           ./templates/template4.png
+
+[HistogramModule.getHistogram]
+limit_to_mask: True
+bins: 20
+
+[BrightContrastModule.getContrast]
+limit_to_mask: True
+
+
+[BrightContrastModule.getBrightnessGray]
+limit_to_mask: True
+
+[BrightContrastModule.getBrightnessByChannelinColorSpace:RGB]
+limit_to_mask: True
+
+
+[BrightContrastModule.getBrightnessByChannelinColorSpace:YUV]
+limit_to_mask: True
+#pick a color space in the list from 'RGB', 'HSV', 'RGB CIE', 'XYZ', 'YUV', 'YIQ', 'YPbPr', 'YCbCr'  : http://scikit-image.org/docs/dev/api/skimage.color.html#skimage.color.convert_colorspace
+to_color_space: YUV
+
+[BrightContrastModule.getContrast:background]
+limit_to_mask: True
+invert: True
+prefix: background
+
+[BrightContrastModule.getBrightnessGray:background]
+limit_to_mask: True
+invert: True
+prefix: background
+
+[BrightContrastModule.getBrightnessByChannelinColorSpace:RGB:background]
+limit_to_mask: True
+invert: True
+prefix: background
+
+[SaveModule.saveFinalMask]
+overlay: True
+
+[SaveModule.saveMacro]
+dim: 500
+
+[SaveModule.saveThumbnails]
+image_work_size: 1.25x
+small_dim: 500
+
+[BlurDetectionModule.identifyBlurryRegions]
+image_work_size = 2.5x
+blur_radius: 100
+blur_threshold: .05
+
+
+[BasicModule.finalComputations]
+
+[BasicModule.finalProcessingSpur]
+disk_radius: 5
+
+[BasicModule.finalProcessingArea]
+#area_threshold: 90000
+area_threshold:  10000
+
+[DeconvolutionModule.separateStains]
+;hed_from_rgb: Hematoxylin + Eosin + DAB
+;hdx_from_rgb: Hematoxylin + DAB
+;fgx_from_rgb: Feulgen + Light Green
+;bex_from_rgb: Giemsa stain : Methyl Blue + Eosin
+;rbd_from_rgb: FastRed + FastBlue + DAB
+;gdx_from_rgb: Methyl Green + DAB
+;hax_from_rgb: Hematoxylin + AEC
+;bro_from_rgb: Blue matrix Anilline Blue + Red matrix Azocarmine + Orange matrix Orange-G
+;bpx_from_rgb: Methyl Blue + Ponceau Fuchsin
+;ahx_from_rgb: Alcian Blue + Hematoxylin
+;hpx_from_rgb: Hematoxylin + PAS
+stain: hed_from_rgb
+use_mask: True
+
+
+[BubbleRegionByRegion.detectSmoothness]
+threshold: .01
+kernel_size: 10
+min_object_size: 500