diff --git a/examples/workflows/alexmac/config.json b/examples/workflows/alexmac/config.json
new file mode 100644
index 0000000000000000000000000000000000000000..52a126c8c803052abfcec272f40f1a4194cbd290
--- /dev/null
+++ b/examples/workflows/alexmac/config.json
@@ -0,0 +1,27 @@
+{
+ "version": "1.0",
+ "installdir": "/home/aknecht/stash/walia/ih/ih/build/scripts-2.7/",
+ "profile": {
+ "pegasus": {
+ "style": "condor"
+ },
+ "condor": {
+ "universe": "vanilla",
+ "requirements": "OSGVO_OS_STRING == \"RHEL 6\" && HAS_FILE_usr_lib64_libstdc___so_6 && CVMFS_oasis_opensciencegrid_org_REVISION >= 3590",
+ "+WantsStashCache": "True"
+ }
+ },
+ "osg": {
+ "tarball": "/home/aknecht/stash/walia/ih/ih/dist/ih-1.0.tar.gz",
+ "ssh": "/home/aknecht/.ssh/workflow"
+ },
+ "cluster": 50,
+ "maxwalltime": {
+ "stats": 300,
+ "images": 3
+ },
+ "notify": {
+ "email": "avi@kurtknecht.com",
+ "pegasus_home": "/usr/share/pegasus/"
+ }
+}
diff --git a/examples/workflows/alexmac/crawl.json b/examples/workflows/alexmac/crawl.json
new file mode 100644
index 0000000000000000000000000000000000000000..635c0e464525080bbeb94f349e1edcf986b553c4
--- /dev/null
+++ b/examples/workflows/alexmac/crawl.json
@@ -0,0 +1,42 @@
+{
+ "path": "/home/aknecht/stash/9-22-15_lemnatec_images/alexmac/%experiment%_%id%-%genotype%_%date%_%null%_%null%/%stype%_%view%_%angle%/0_0_0.png",
+ "base": "/home/aknecht/stash/9-22-15_lemnatec_images/alexmac/",
+ "filetype": ".png",
+ "order": ["experiment", "id", "genotype", "date", "imgname", "imtype", "path"],
+ "translations": {
+ "imtype": {
+ "fluo_sv": "fluosv",
+ "vis_tv": "rgbtv",
+ "vis_sv": "rgbsv"
+ }
+ },
+ "data": {
+ "experiment": {
+ "type": "value",
+ "value": "%experiment%"
+ },
+ "id": {
+ "type": "value",
+ "value": "%id%"
+ },
+ "genotype": {
+ "type": "value",
+ "value": "%genotype%"
+ },
+ "date": {
+ "type": "date",
+ "value": "%date%",
+ "format": "Y-m-d"
+ },
+ "imtype": {
+ "type": "value",
+ "translate": "true",
+ "value": "%stype%_%view%",
+ "case": "lower"
+ },
+ "imgname": {
+ "type": "value",
+ "value": "%stype%_%view%_%angle%"
+ }
+ }
+}
diff --git a/examples/workflows/alexmac/fluosv_edge.json b/examples/workflows/alexmac/fluosv_edge.json
new file mode 100644
index 0000000000000000000000000000000000000000..03f1ef17653f8d73828ff7dfb161610b18ad1ab9
--- /dev/null
+++ b/examples/workflows/alexmac/fluosv_edge.json
@@ -0,0 +1,6 @@
+{
+ "ystart": 590,
+ "yend": 1190,
+ "xstart": 219,
+ "xend": 799
+}
diff --git a/examples/workflows/alexmac/imgproc.json b/examples/workflows/alexmac/imgproc.json
new file mode 100644
index 0000000000000000000000000000000000000000..d73feb4e9a2bf1535609d838ab3dd5609b6d7aeb
--- /dev/null
+++ b/examples/workflows/alexmac/imgproc.json
@@ -0,0 +1,348 @@
+{
+ "workflows": {
+
+ "fluosv": [
+ {
+ "name": "gray",
+ "executable": "ih-convert-color",
+ "inputs": ["base"],
+ "outputs": ["grayscale"],
+ "arguments": {
+ "--intype": "bgr",
+ "--outtype": "gray"
+ }
+ },
+ {
+ "name": "blur",
+ "executable": "ih-gaussian-blur",
+ "inputs": ["grayscale"],
+ "outputs": ["blurred"],
+ "arguments": {
+ "--kwidth": 5,
+ "--kheight": 5
+ },
+ "depends": ["gray"]
+ },
+ {
+ "name": "thresh",
+ "executable": "ih-threshold",
+ "inputs": ["blurred"],
+ "outputs": ["masked"],
+ "arguments": {
+ "--thresh": 0,
+ "--max": 255,
+ "--type": "otsu"
+ },
+ "depends": ["blur"]
+ },
+ {
+ "name": "reconstitute",
+ "executable": "ih-bitwise-and",
+ "inputs": ["masked", "base"],
+ "outputs": ["recolor"],
+ "arguments": {},
+ "depends": ["thresh"]
+ },
+ {
+ "name": "crop",
+ "executable": "ih-crop",
+ "inputs": ["recolor", "/home/aknecht/stash/walia/ih/workflows/alexmac/input/fluosv_edge.json"],
+ "outputs": ["edged"],
+ "arguments": {},
+ "depends": ["reconstitute"]
+ },
+ {
+ "name": "cut",
+ "executable": "ih-contour-cut",
+ "inputs": ["edged", "edged"],
+ "outputs": ["final"],
+ "arguments": {
+ "--resize": "",
+ "--basemin": 50
+ },
+ "depends": ["crop"]
+ }
+ ],
+
+
+
+ "rgbtv": [
+ {
+ "name": "blur",
+ "executable": "ih-gaussian-blur",
+ "inputs": ["base"],
+ "outputs": ["blurred"],
+ "arguments": {
+ "--kwidth": 13,
+ "--kheight": 13
+ }
+ },
+ {
+ "name": "sharpen",
+ "executable": "ih-add-weighted",
+ "inputs": ["base", "blurred"],
+ "outputs": ["sharpened"],
+ "arguments": {
+ "--weight1": 1.5,
+ "--weight2": -0.5
+ },
+ "depends": ["blur"]
+ },
+ {
+ "name": "crop",
+ "executable": "ih-crop",
+ "inputs": ["sharpened", "/home/aknecht/stash/walia/ih/workflows/alexmac/input/rgbtv_edge.json"],
+ "outputs": ["edged"],
+ "arguments": {},
+ "depends": ["sharpen"]
+ },
+ {
+ "name": "cfilter1",
+ "executable": "ih-color-filter",
+ "inputs": ["edged"],
+ "outputs": ["cf1"],
+ "arguments": {
+ "--logic": "((r > b) or ((g > r) and ((g - b) > 10)))"
+ },
+ "depends": ["crop"]
+ },
+ {
+ "name": "bgr_lab",
+ "executable": "ih-convert-color",
+ "inputs": ["cf1"],
+ "outputs": ["lab_spectrum"],
+ "arguments": {
+ "--intype": "bgr",
+ "--outtype": "lab"
+ },
+ "depends": ["cfilter1"]
+ },
+ {
+ "name": "labfilter1",
+ "executable": "ih-color-filter",
+ "inputs": ["lab_spectrum"],
+ "outputs": ["lf1"],
+ "arguments": {
+ "--logic": "((r - g) > 5)"
+ },
+ "depends": ["bgr_lab"]
+ },
+ {
+ "name": "labfilter2",
+ "executable": "ih-color-filter",
+ "inputs": ["lf1"],
+ "outputs": ["lf2"],
+ "arguments": {
+ "--logic": "((r > b) and (g > b))"
+ },
+ "depends": ["labfilter1"]
+ },
+ {
+ "name": "mask",
+ "executable": "ih-mask",
+ "inputs": ["lf2"],
+ "outputs": ["masked"],
+ "arguments": {},
+ "depends": ["labfilter2"]
+ },
+ {
+ "name": "reconstitute",
+ "executable": "ih-bitwise-and",
+ "inputs": ["masked", "base"],
+ "outputs": ["recolor"],
+ "arguments": {},
+ "depends": ["mask"]
+ },
+ {
+ "name": "cfilter2",
+ "executable": "ih-color-filter",
+ "inputs": ["recolor"],
+ "outputs": ["cf2"],
+ "arguments": {
+ "--logic": "(((r - g) < ((i * i) / 4000)) or (((r - g) > (40 * (1 - (i / 765)))) and ((r - b) > (60 * (1 - (i / 765))))))"
+ },
+ "depends": ["reconstitute"]
+ },
+ {
+ "name": "erode",
+ "executable": "ih-morphology",
+ "inputs": ["cf2"],
+ "outputs": ["morph_erode"],
+ "arguments": {
+ "--ktype": "ellipse",
+ "--kwidth": 3,
+ "--kheight": 3,
+ "--morphType": "erode"
+ },
+ "depends": ["cfilter2"]
+ },
+ {
+ "name": "contour_chop",
+ "executable": "ih-contour-chop",
+ "inputs": ["morph_erode", "morph_erode"],
+ "outputs": ["chop"],
+ "arguments": {
+ "--basemin": 100
+ },
+ "depends": ["erode"]
+ },
+ {
+ "name": "mask2",
+ "executable": "ih-mask",
+ "inputs": ["chop"],
+ "outputs": ["mask2"],
+ "arguments": {},
+ "depends": ["contour_chop"]
+ },
+ {
+ "name": "dilate",
+ "executable": "ih-morphology",
+ "inputs": ["mask2"],
+ "outputs": ["morph_dilate"],
+ "arguments": {
+ "--ktype": "ellipse",
+ "--kwidth": 3,
+ "--kheight": 3,
+ "--morphType": "dilate"
+ },
+ "depends": ["mask2"]
+ },
+ {
+ "name": "reconstitute2",
+ "executable": "ih-bitwise-and",
+ "inputs": ["morph_dilate", "base"],
+ "outputs": ["recolor2"],
+ "arguments": {},
+ "depends": ["dilate"]
+ },
+ {
+ "name": "cut",
+ "executable": "ih-contour-cut",
+ "inputs": ["recolor2", "recolor2"],
+ "outputs": ["final"],
+ "arguments": {
+ "--basemin": 100,
+ "--resize": ""
+ },
+ "depends": ["reconstitute2"]
+ }
+ ],
+ "rgbsv": [
+ {
+ "name": "gray",
+ "executable": "ih-convert-color",
+ "inputs": ["base"],
+ "outputs": ["grayscale"],
+ "arguments": {
+ "--intype": "bgr",
+ "--outtype": "gray"
+ }
+ },
+ {
+ "name": "blur",
+ "executable": "ih-gaussian-blur",
+ "inputs": ["grayscale"],
+ "outputs": ["blurred"],
+ "arguments": {
+ "--kwidth": 5,
+ "--kheight": 5
+ },
+ "depends": ["gray"]
+ },
+ {
+ "name": "thresh",
+ "executable": "ih-adaptive-threshold",
+ "inputs": ["blurred"],
+ "outputs": ["thresh"],
+ "arguments": {
+ "--value": 255,
+ "--thresholdType": "inverse",
+ "--adaptiveType": "mean",
+ "--blockSize": 15,
+ "--C": 6
+ },
+ "depends": ["blur"]
+ },
+ {
+ "name": "reconstitute",
+ "executable": "ih-bitwise-and",
+ "inputs": ["thresh", "base"],
+ "outputs": ["recolor"],
+ "arguments": {},
+ "depends": ["thresh"]
+ },
+ {
+ "name": "crop",
+ "executable": "ih-crop",
+ "inputs": ["recolor", "/home/aknecht/stash/walia/ih/workflows/alexmac/input/rgbsv_edge.json"],
+ "outputs": ["edged"],
+ "arguments": {},
+ "depends": ["reconstitute"]
+ },
+ {
+ "name": "fill",
+ "executable": "ih-fill",
+ "inputs": ["edged", "/home/aknecht/stash/walia/ih/workflows/alexmac/input/rgbsv_pot.json"],
+ "outputs": ["filled"],
+ "arguments": {},
+ "depends": ["crop"]
+ },
+ {
+ "name": "cut",
+ "executable": "ih-contour-cut",
+ "inputs": ["filled", "filled"],
+ "outputs": ["final"],
+ "arguments": {
+ "--basemin": 50,
+ "--resize": ""
+ },
+ "depends": ["fill"]
+ }
+ ]
+ },
+ "options": {
+
+ },
+ "extract": {
+ "histogram-bin": {
+ "--group": {"rgb": ["rgbsv", "rgbtv"], "fluo": ["fluosv"]},
+ "--chunks": {"rgb": [5, 5, 5], "fluo": [0, 9, 10]},
+ "--channels": {"rgb": [0, 1, 2], "fluo": [1, 2]}
+ },
+ "workflows": {
+ "rgbsv": {
+ "inputs": ["final"],
+ "arguments": {
+ "--dimensions": "",
+ "--pixels": "",
+ "--moments": "",
+ "--circle": "",
+ "--hull": ""
+ },
+ "depends": ["cut"]
+ },
+ "rgbtv": {
+ "inputs": ["final"],
+ "arguments": {
+ "--dimensions": "",
+ "--pixels": "",
+ "--moments": "",
+ "--circle": "",
+ "--hull": ""
+ },
+ "depends": ["cut"]
+ },
+ "fluosv": {
+ "inputs": ["final"],
+ "arguments": {
+ "--dimensions": "",
+ "--pixels": "",
+ "--moments": "",
+ "--circle": "",
+ "--hull": ""
+ },
+ "depends": ["cut"]
+ }
+ }
+ }
+}
diff --git a/examples/workflows/alexmac/rgbsv_edge.json b/examples/workflows/alexmac/rgbsv_edge.json
new file mode 100644
index 0000000000000000000000000000000000000000..390309028720ceb22a242199335af50dc56bda75
--- /dev/null
+++ b/examples/workflows/alexmac/rgbsv_edge.json
@@ -0,0 +1,6 @@
+{
+ "ystart": 400,
+ "yend": "y",
+ "xstart": 400,
+ "xend": "x - 400"
+}
diff --git a/examples/workflows/alexmac/rgbsv_pot.json b/examples/workflows/alexmac/rgbsv_pot.json
new file mode 100644
index 0000000000000000000000000000000000000000..1b72c0bd2de7f31ecd09d290388877fc187b5612
--- /dev/null
+++ b/examples/workflows/alexmac/rgbsv_pot.json
@@ -0,0 +1,6 @@
+{
+ "ystart": 1746,
+ "yend": 2056,
+ "xstart": 992,
+ "xend": 1572
+}
diff --git a/examples/workflows/alexmac/rgbtv_edge.json b/examples/workflows/alexmac/rgbtv_edge.json
new file mode 100644
index 0000000000000000000000000000000000000000..04353d46377e23d1d874b7fa4b1a527ac0b959d4
--- /dev/null
+++ b/examples/workflows/alexmac/rgbtv_edge.json
@@ -0,0 +1,6 @@
+{
+ "ystart": 350,
+ "yend": "y - 350",
+ "xstart": 350,
+ "xend": "x - 350"
+}
diff --git a/examples/workflows/blecha/config.json b/examples/workflows/blecha/config.json
new file mode 100644
index 0000000000000000000000000000000000000000..52a126c8c803052abfcec272f40f1a4194cbd290
--- /dev/null
+++ b/examples/workflows/blecha/config.json
@@ -0,0 +1,27 @@
+{
+ "version": "1.0",
+ "installdir": "/home/aknecht/stash/walia/ih/ih/build/scripts-2.7/",
+ "profile": {
+ "pegasus": {
+ "style": "condor"
+ },
+ "condor": {
+ "universe": "vanilla",
+ "requirements": "OSGVO_OS_STRING == \"RHEL 6\" && HAS_FILE_usr_lib64_libstdc___so_6 && CVMFS_oasis_opensciencegrid_org_REVISION >= 3590",
+ "+WantsStashCache": "True"
+ }
+ },
+ "osg": {
+ "tarball": "/home/aknecht/stash/walia/ih/ih/dist/ih-1.0.tar.gz",
+ "ssh": "/home/aknecht/.ssh/workflow"
+ },
+ "cluster": 50,
+ "maxwalltime": {
+ "stats": 300,
+ "images": 3
+ },
+ "notify": {
+ "email": "avi@kurtknecht.com",
+ "pegasus_home": "/usr/share/pegasus/"
+ }
+}
diff --git a/examples/workflows/blecha/crawl.json b/examples/workflows/blecha/crawl.json
new file mode 100644
index 0000000000000000000000000000000000000000..dc5a4809add47f77cb84197a840823d564115092
--- /dev/null
+++ b/examples/workflows/blecha/crawl.json
@@ -0,0 +1,42 @@
+{
+ "path": "/home/aknecht/stash/9-22-15_lemnatec_images/Blecha 81315/%experiment%_%id%-%genotype%_%date%_%null%_%null%/%stype%_%view%_%angle%/0_0_0.png",
+ "base": "/home/aknecht/stash/9-22-15_lemnatec_images/Blecha 81315/",
+ "filetype": ".png",
+ "order": ["experiment", "id", "genotype", "date", "imgname", "imtype", "path"],
+ "translations": {
+ "imtype": {
+ "fluo_sv": "fluosv",
+ "vis_tv": "rgbtv",
+ "vis_sv": "rgbsv"
+ }
+ },
+ "data": {
+ "experiment": {
+ "type": "value",
+ "value": "%experiment%"
+ },
+ "id": {
+ "type": "value",
+ "value": "%id%"
+ },
+ "genotype": {
+ "type": "value",
+ "value": "%genotype%"
+ },
+ "date": {
+ "type": "date",
+ "value": "%date%",
+ "format": "Y-m-d"
+ },
+ "imtype": {
+ "type": "value",
+ "translate": "true",
+ "value": "%stype%_%view%",
+ "case": "lower"
+ },
+ "imgname": {
+ "type": "value",
+ "value": "%stype%_%view%_%angle%"
+ }
+ }
+}
diff --git a/examples/workflows/blecha/fluosv_edge.json b/examples/workflows/blecha/fluosv_edge.json
new file mode 100644
index 0000000000000000000000000000000000000000..03f1ef17653f8d73828ff7dfb161610b18ad1ab9
--- /dev/null
+++ b/examples/workflows/blecha/fluosv_edge.json
@@ -0,0 +1,6 @@
+{
+ "ystart": 590,
+ "yend": 1190,
+ "xstart": 219,
+ "xend": 799
+}
diff --git a/examples/workflows/blecha/imgproc.json b/examples/workflows/blecha/imgproc.json
new file mode 100644
index 0000000000000000000000000000000000000000..4583089e0d7134a945e8f4f830954c0f5e8a703c
--- /dev/null
+++ b/examples/workflows/blecha/imgproc.json
@@ -0,0 +1,320 @@
+{
+ "workflows": {
+ "rgbtv": [
+ {
+ "name": "normalize",
+ "executable": "ih-normalize-intensity",
+ "inputs": ["base"],
+ "outputs": ["normal"],
+ "arguments": {}
+ },
+ {
+ "name": "crop_center",
+ "executable": "ih-crop",
+ "inputs": ["normal", "rgbtv_center.json"],
+ "outputs": ["centeronly"],
+ "arguments": {},
+ "depends": ["normalize"]
+ },
+ {
+ "name": "green_filter",
+ "executable": "ih-color-filter",
+ "inputs": ["centeronly"],
+ "outputs": ["gfilter"],
+ "arguments": {
+ "--logic": "(((g - r) > 15) and ((g - b) > 15))"
+ },
+ "depends": ["crop_center"]
+ },
+ {
+ "name": "create_seed_mask",
+ "executable": "ih-mask",
+ "inputs": ["gfilter"],
+ "outputs": ["seedmask"],
+ "arguments": {},
+ "depends": ["green_filter"]
+ },
+ {
+ "name": "blur",
+ "executable": "ih-blur",
+ "inputs": ["normal"],
+ "outputs": ["blurred"],
+ "arguments": {
+ "--kwidth": 3,
+ "--kheight": 3
+ },
+ "depends": ["normalize"]
+ },
+ {
+ "name": "sharpen",
+ "executable": "ih-add-weighted",
+ "inputs": ["normal", "blurred"],
+ "outputs": ["sharpened"],
+ "arguments": {
+ "--weight1": 1.5,
+ "--weight2": -0.5
+ },
+ "depends": ["blur"]
+ },
+ {
+ "name": "extract_green",
+ "executable": "ih-split",
+ "inputs": ["sharpened"],
+ "outputs": ["gchannel"],
+ "arguments": {
+ "--channel": 1
+ },
+ "depends": ["sharpen"]
+ },
+ {
+ "name": "equalize",
+ "executable": "ih-equalize-hist",
+ "inputs": ["gchannel"],
+ "outputs": ["equalized"],
+ "arguments": {},
+ "depends": ["extract_green"]
+ },
+ {
+ "name": "bg_cfilter",
+ "executable": "ih-color-filter",
+ "inputs": ["normal"],
+ "outputs": ["bg_noise"],
+ "arguments": {
+ "--logic": "(((high - low) < (i / 30)) or ((b - r) > (i / 10)))"
+ },
+ "depends": ["normalize"]
+ },
+ {
+ "name": "bgmask",
+ "executable": "ih-mask",
+ "inputs": ["bg_noise"],
+ "outputs": ["bg_mask"],
+ "arguments": {},
+ "depends": ["bg_cfilter"]
+ },
+ {
+ "name": "flood",
+ "executable": "ih-flood-fill",
+ "inputs": ["equalized", "bg_mask", "seedmask"],
+ "outputs": ["flooded"],
+ "arguments": {
+ "--low": "50",
+ "--high": "50",
+ "--writecolor": "255",
+ "--connectivity": 8,
+ "--findSeed": "",
+ "--binary": ""
+ },
+ "depends": ["equalize", "bgmask", "create_seed_mask"]
+ },
+ {
+ "name": "thresh",
+ "executable": "ih-threshold",
+ "inputs": ["flooded"],
+ "outputs": ["flood_binary"],
+ "arguments": {
+ "--thresh": 254,
+ "--type": "inverse"
+ },
+ "depends": ["flood"]
+ },
+ {
+ "name": "combine_with_mask",
+ "executable": "ih-bitwise-or",
+ "inputs": ["flood_binary", "bgmask"],
+ "outputs": ["invmask"],
+ "arguments": {},
+ "depends": ["thresh"]
+ },
+ {
+ "name": "invert",
+ "executable": "ih-bitwise-not",
+ "inputs": ["invmask"],
+ "outputs": ["premask"],
+ "arguments": {},
+ "depends": ["combine_with_mask"]
+ },
+ {
+ "name": "crop_edges",
+ "executable": "ih-crop",
+ "inputs": ["premask", "rgbtv_edge.json"],
+ "outputs": ["edged_mask"],
+ "depends": ["invert"]
+ },
+ {
+ "name": "chop",
+ "executable": "ih-contour-chop",
+ "inputs": ["edged_mask", "edged_mask"],
+ "outputs": ["chopped"],
+ "arguments": {
+ "--basemin": 50
+ },
+ "depends": ["crop_edges"]
+ },
+ {
+ "name": "erode",
+ "executable": "ih-morphology",
+ "inputs": ["chopped"],
+ "outputs": ["morph_erode"],
+ "arguments": {
+ "--ktype": "ellipse",
+ "--kwidth": 3,
+ "--kheight": 3,
+ "--morphType": "erode"
+ },
+ "depends": ["chop"]
+ },
+ {
+ "name": "dilate",
+ "executable": "ih-morphology",
+ "inputs": ["morph_erode"],
+ "outputs": ["morph_dilate"],
+ "arguments": {
+ "--ktype": "ellipse",
+ "--kwidth": 3,
+ "--kheight": 3,
+ "--morphType": "dilate"
+ },
+ "depends": ["erode"]
+ },
+ {
+ "name": "reconstitute",
+ "executable": "ih-bitwise-and",
+ "inputs": ["morph_dilate", "base"],
+ "outputs": ["recolor"],
+ "arguments": {},
+ "depends": ["dilate"]
+ },
+ {
+ "name": "cut",
+ "executable": "ih-contour-cut",
+ "inputs": ["recolor", "recolor"],
+ "outputs": ["final"],
+ "arguments": {
+ "--basemin": 50,
+ "--resize": ""
+ },
+ "depends": ["reconstitute"]
+ }
+ ],
+ "rgbsv": [
+ {
+ "name": "normalize",
+ "executable": "ih-normalize-intensity",
+ "inputs": ["base"],
+ "outputs": ["normal"],
+ "arguments": {}
+ },
+ {
+ "name": "blur",
+ "executable": "ih-gaussian-blur",
+ "inputs": ["normal"],
+ "outputs": ["blurred"],
+ "arguments": {
+ "--kwidth": 5,
+ "--kheight": 5
+ },
+ "depends": ["normalize"]
+ },
+ {
+ "name": "gray_filter",
+ "executable": "ih-color-filter",
+ "inputs": ["blurred"],
+ "outputs": ["gfiltered"],
+ "arguments": {
+ "--logic": "((high - low) > (i / 30))"
+ },
+ "depends": ["blur"]
+ },
+ {
+ "name": "pot_filter",
+ "executable": "ih-color-filter",
+ "inputs": ["gfiltered"],
+ "outputs": ["pfiltered"],
+ "arguments": {
+ "--logic": "((g > b) and (g > r))"
+ },
+ "depends": ["gray_filter"]
+ },
+ {
+ "name": "box_filter",
+ "executable": "ih-color-filter",
+ "inputs": ["pfiltered"],
+ "outputs": ["bfiltered"],
+ "arguments": {
+ "--logic": "((g > b) and (g > r))"
+ },
+ "depends": ["pot_filter"]
+ },
+ {
+ "name": "crop",
+ "executable": "ih-crop",
+ "inputs": ["bfiltered", "rgbsv_edge.json"],
+ "outputs": ["edged"],
+ "arguments": {},
+ "depends": ["box_filter"]
+ },
+ {
+ "name": "mask",
+ "executable": "ih-mask",
+ "inputs": ["edged"],
+ "outputs": ["fmask"],
+ "arguments": {},
+ "depends": ["crop"]
+ },
+ {
+ "name": "reconstitute",
+ "executable": "ih-bitwise-and",
+ "inputs": ["fmask"],
+ "outputs": ["recolor"],
+ "arguments": {},
+ "depends": ["mask"]
+ },
+ {
+ "name": "cut",
+ "executable": "ih-contour-cut",
+ "inputs": ["recolor", "recolor"],
+ "outputs": ["final"],
+ "arguments": {
+ "--basemin": 50,
+ "--resize": ""
+ },
+ "depends": ["reconstitute"]
+ }
+ ]
+ },
+ "options": {
+
+ },
+ "extract": {
+ "histogram-bin": {
+ "--group": {"rgb": ["rgbsv", "rgbtv"], "fluo": ["fluosv"]},
+ "--chunks": {"rgb": [5, 5, 5], "fluo": [0, 9, 10]},
+ "--channels": {"rgb": [0, 1, 2], "fluo": [1, 2]}
+ },
+ "workflows": {
+ "rgbsv": {
+ "inputs": ["final"],
+ "arguments": {
+ "--dimensions": "",
+ "--pixels": "",
+ "--moments": "",
+ "--circle": "",
+ "--hull": ""
+ },
+ "depends": ["cut"]
+ },
+ "rgbtv": {
+ "inputs": ["final"],
+ "arguments": {
+ "--dimensions": "",
+ "--pixels": "",
+ "--moments": "",
+ "--circle": "",
+ "--hull": ""
+ },
+ "depends": ["cut"]
+ }
+ }
+ }
+}
diff --git a/examples/workflows/blecha/rgbsv_box.json b/examples/workflows/blecha/rgbsv_box.json
new file mode 100644
index 0000000000000000000000000000000000000000..548ab9d4757764d89a00e2b37161d640ef44d010
--- /dev/null
+++ b/examples/workflows/blecha/rgbsv_box.json
@@ -0,0 +1,6 @@
+{
+ "ystart": 1931,
+ "yend": 2056,
+ "xstart": 1037,
+ "xstart": 1557
+}
diff --git a/examples/workflows/blecha/rgbsv_edge.json b/examples/workflows/blecha/rgbsv_edge.json
new file mode 100644
index 0000000000000000000000000000000000000000..8c64f5ddf595d88558864eac9370ef6a3962ce89
--- /dev/null
+++ b/examples/workflows/blecha/rgbsv_edge.json
@@ -0,0 +1,6 @@
+{
+ "ystart": 1000,
+ "yend": "y",
+ "xstart": 400,
+ "xend": "x - 400"
+}
diff --git a/examples/workflows/blecha/rgbsv_pot.json b/examples/workflows/blecha/rgbsv_pot.json
new file mode 100644
index 0000000000000000000000000000000000000000..dbe7132b0e8c648c04b86bf8f6b84af65beb1ba5
--- /dev/null
+++ b/examples/workflows/blecha/rgbsv_pot.json
@@ -0,0 +1,6 @@
+{
+ "ystart": 1806,
+ "yend": 2056,
+ "xstart": 1107,
+ "xend": 1487
+}
diff --git a/examples/workflows/blecha/rgbtv_center.json b/examples/workflows/blecha/rgbtv_center.json
new file mode 100644
index 0000000000000000000000000000000000000000..a76caaf02b93e9c25fdd24252ff7f95f41a5d148
--- /dev/null
+++ b/examples/workflows/blecha/rgbtv_center.json
@@ -0,0 +1,6 @@
+{
+ "ystart": 740,
+ "yend": 1350,
+ "xstart": 900,
+ "xend": 1520
+}
diff --git a/examples/workflows/blecha/rgbtv_edge.json b/examples/workflows/blecha/rgbtv_edge.json
new file mode 100644
index 0000000000000000000000000000000000000000..c48375dfd1867cccab4c689041eef534f8447671
--- /dev/null
+++ b/examples/workflows/blecha/rgbtv_edge.json
@@ -0,0 +1,6 @@
+{
+ "ystart": 200,
+ "yend": "y - 200",
+ "xstart": 200,
+ "xend": "x - 200"
+}
diff --git a/examples/workflows/blecha/stats.json b/examples/workflows/blecha/stats.json
new file mode 100644
index 0000000000000000000000000000000000000000..ee72e6a9b721f90e52bf37f6e2fb160cc48520e8
--- /dev/null
+++ b/examples/workflows/blecha/stats.json
@@ -0,0 +1,36 @@
+{
+ "rgb": [
+ {
+ "name": "area",
+ "executable": "pcv-stats-shoot-area",
+ "inputs": ["images"],
+ "outputs": ["shootarea"],
+ "arguments": {
+ "--group": {
+ "rgb": ["rgbsv"]
+ }
+ },
+ "depends": ["bin"]
+ },
+ {
+ "name": "normal",
+ "executable": "pcv-stats-normalize",
+ "inputs": ["shootarea"],
+ "outputs": ["normal"],
+ "arguments": {
+ "--column": "pixels"
+ },
+ "depends": ["area"]
+ },
+ {
+ "name": "threshold",
+ "executable": "pcv-stats-threshold",
+ "inputs": ["normal"],
+ "outputs": ["thresh"],
+ "arguments": {
+ "--thresh": 0.01
+ },
+ "depends": ["normal"]
+ }
+ ]
+}
diff --git a/ih/conf.py b/ih/conf.py
index 01db04df782ba715f5a25512a7f4e8b2b72a0f7c..fb7da9c7703fec977addea51ea7ea437d9efab02 100644
--- a/ih/conf.py
+++ b/ih/conf.py
@@ -73,6 +73,7 @@ adaptives = {
"gaussian": cv2.ADAPTIVE_THRESH_GAUSSIAN_C
}
+
"""
A dictionary used to map border-types to cv2 border codes
"""
@@ -617,6 +618,136 @@ valid = {
}
}
},
+ "ih-split": {
+ "type": "imgproc",
+ "inputs": ["image"],
+ "outputs": ["image"],
+ "arguments": {
+ "--input": {
+ "type": "derived",
+ "key": "inputs",
+ "index": 0,
+ "required": "true"
+ },
+ "--output": {
+ "type": "derived",
+ "key": "outputs",
+ "index": 0,
+ "required": "true"
+ },
+ "--outputdir": {
+ "type": "overwrite",
+ "value": "."
+ },
+ "--writeblank": {
+ "type": "overwrite",
+ "required": "true",
+ "value": ""
+ },
+ "--channel": {
+ "type": "numeric",
+ "validation": "list",
+ "value": [0, 1, 2],
+ "required": "true"
+ }
+ }
+ },
+ "ih-equalize-hist": {
+ "type": "imgproc",
+ "inputs": ["image"],
+ "outputs": ["image"],
+ "arguments": {
+ "--input": {
+ "type": "derived",
+ "key": "inputs",
+ "index": 0,
+ "required": "true"
+ },
+ "--output": {
+ "type": "derived",
+ "key": "outputs",
+ "index": 0,
+ "required": "true"
+ },
+ "--outputdir": {
+ "type": "overwrite",
+ "value": "."
+ },
+ "--writeblank": {
+ "type": "overwrite",
+ "required": "true",
+ "value": ""
+ }
+ }
+ },
+ "ih-flood-fill": {
+ "type": "imgproc",
+ "inputs": ["image", "image", "image"],
+ "outputs": ["image"],
+ "arguments": {
+ "--input": {
+ "type": "derived",
+ "key": "inputs",
+ "index": 0,
+ "required": "true"
+ },
+ "--mask": {
+ "type": "derived",
+ "key": "inputs",
+ "index": 1,
+ "required": "true"
+ },
+ "--seedMask": {
+ "type": "derived",
+ "key": "inputs",
+ "index": 2
+ },
+ "--output": {
+ "type": "derived",
+ "key": "outputs",
+ "index": 0,
+ "required": "true"
+ },
+ "--outputdir": {
+ "type": "overwrite",
+ "value": "."
+ },
+ "--writeblank": {
+ "type": "overwrite",
+ "required": "true",
+ "value": ""
+ },
+ "--low": {
+ "type": "string",
+ "required": "true"
+ },
+ "--high": {
+ "type": "string",
+ "required": "true"
+ },
+ "--writeColor": {
+ "type": "string",
+ "required": "true"
+ },
+ "--connectivity": {
+ "type": "numeric",
+ "validation": "list",
+ "value": [4, 8]
+ },
+ "--fixed": {
+ "type": "exist"
+ },
+ "--seedx": {
+ "type": "numeric"
+ },
+ "--seedy": {
+ "type": "numeric"
+ },
+ "--findSeed": {
+ "type": "exist"
+ }
+ }
+ },
"ih-fill": {
"type": "imgproc",
"inputs": ["image", "roi"],
diff --git a/ih/imgproc.py b/ih/imgproc.py
index d6c96d8c9f7b1e07afe1639d7a7a3f6d6bf122b9..3d2d7e7f57a4d41b4b349d1b265159d822f0f721 100644
--- a/ih/imgproc.py
+++ b/ih/imgproc.py
@@ -421,6 +421,16 @@ class Image(object):
self.destroy()
return
+ def split(self, channel):
+ self.image = cv2.split(self.image)[channel]
+ return
+
+ def equalizeHist(self):
+ if self._isColor():
+ self.image = cv2.cvtColor(self.image, cv2.COLOR_BGR2GRAY)
+ self.image = cv2.equalizeHist(self.image)
+ return
+
def show(self, title = None, state = None):
"""
:param title: The title to give the display window, if left blank one will be created.
@@ -821,6 +831,76 @@ class Image(object):
else:
raise Exception("Invalid morphology type, should be one of: " + ",".join(conf.morph.keys()) + ".")
+ def _findSeed(self, seedMask):
+ bname, binary = self._loadResource(seedMask)
+ if self._isColor(binary):
+ binary = cv2.cvtColor(binary, cv2.COLOR_BGR2GRAY)
+ contours, hierarchy = cv2.findContours(binary, cv2.RETR_EXTERNAL, 2)
+ size = 0
+ select = 0
+ for cnt in contours:
+ if cv2.contourArea(cnt) > size:
+ select = cnt
+ size = cv2.contourArea(cnt)
+ return tuple(select[0][0])
+
+ def floodFill(self, mask, low, high, writeColor = (255, 255, 255), connectivity = 4, fixed = False, seed = (0,0), findSeed = False, seedMask = None, binary = False):
+ """
+ :param mask: A binary image corresponding to the area you don't want to fill.
+ :type mask: str or np.ndarray
+ :param seed: The beginning point to use for filling.
+ :type seed: Tuple (x, y)
+ :param low: Maximal lower brightness/color difference between the currently observed pixel and one of its neighbors belonging to the component, or a seed pixel being added to the component.
+ :type low: Tuple (b, g, r) or (i,)
+ :param high: Maximal upper brightness/color difference between the currently observed pixel and one of its neighbors belonging to the component, or a seed pixel being added to the component.
+ :type high: Tuple (b, g, r) or (i,)
+ :param writeColor: The color to write to the filled region. Default (255, 255, 255).
+ :type writeColor: tuple (b, g, r) or (i,)
+ :param connectivity: The number of neighboring pixels to consider for the flooding operation. Should be 4 or 8.
+ :type connectivity: int
+ :param fixed: If True, calculates color differences relative to the seed.
+ :type fixed: boolean
+ :param findSeed: If True, picks a seed point based on contours in the seedMask image.
+ :type findSeed: boolean
+ :param seedMask: Binary image to select seed from.
+ :type seedMask: str or np.ndarray
+ :param binary: Specify if input image is binary.
+ :type binary: boolean
+
+ This function is a wrapper to the OpenCV function `floodFill <http://docs.opencv.org/2.4/modules/imgproc/doc/miscellaneous_transformations.html#floodfill>`_.
+ This function floods the region of an image based on calculated color differences from neighbors or from the seed. When flooding a binary
+ image all input color tuples should have 1 value instead of 3.
+ """
+ print low,high,writeColor
+ mname, mask = self._loadResource(mask)
+ if self._isColor(mask):
+ mask = cv2.cvtColor(mask, cv2.COLOR_BGR2GRAY)
+ if binary and self._isColor():
+ self.convertColor("bgr", "gray")
+ # Mask is required to be 2 pixels wider and taller than the image
+ adjmask = np.zeros((self.y + 2, self.x + 2), np.uint8)
+ adjmask[1:1+self.y, 1:1+self.x] = mask
+ channels = 3 if len(self.image.shape) == 3 else 1
+ if len(low) == channels:
+ if len(high) == channels:
+ if len(writeColor) == channels:
+ if connectivity == 4 or connectivity == 8:
+ if findSeed and seedMask:
+ seed = self._findSeed(seedMask)
+ if fixed:
+ cv2.floodFill(self.image, adjmask, seed, writeColor, low, high, connectivity | cv2.FLOODFILL_FIXED_RANGE)
+ else:
+ cv2.floodFill(self.image, adjmask, seed, writeColor, low, high, connectivity)
+ else:
+ raise Exception("Invalid value for connectivity, should be either 4 or 8.")
+ else:
+ raise Exception("Incorrect number of values for write color. Number of values should match input image channels (%s)" % (channels,))
+ else:
+ raise Exception("Incorrect number of values for high difference. Number of values should match input image channels (%s)" % (channels,))
+ else:
+ raise Exception("Incorrect number of values for low difference. Number of values should match input image channels (%s)" % (channels,))
+ return
+
def fill(self, roi, color):
"""
:param roi: A list corresponding to the area of the image you want. List should be of the form [ystart, yend, xstart, xend]
diff --git a/scripts/ih-equalize-hist b/scripts/ih-equalize-hist
new file mode 100644
index 0000000000000000000000000000000000000000..2bc81e61e49f66e1b6286b30b3e70d93ae06e208
--- /dev/null
+++ b/scripts/ih-equalize-hist
@@ -0,0 +1,21 @@
+#!python
+import argparse
+import traceback
+import ih.imgproc
+
+parser = argparse.ArgumentParser(description = "Stretches a grayscale image to the full 0-255 intensity range.")
+parser.add_argument("--input", dest="input", help="Path to input image.", required = True)
+parser.add_argument("--outputdir", dest="outputdir", default=".", help="Path to write output files, if not specified use current directory.")
+parser.add_argument("--output", default=None, dest="output", help="Name of output image to write, if not specified, use input image name.")
+parser.add_argument("--writeblank", default=False, action="store_true", help="If errors happen, write a blank file. Used to ensure dependent files exist for pegasus workflows.")
+args = parser.parse_args()
+
+try:
+ plant = ih.imgproc.Image(args.input, args.outputdir, args.output, False)
+ plant.equalizeHist()
+ plant.write()
+except Exception as e:
+ print traceback.format_exc()
+ if args.writeblank:
+ with open(args.outputdir + "/" + args.output, "w") as wh:
+ wh.write("not an image.")
diff --git a/scripts/ih-flood-fill b/scripts/ih-flood-fill
new file mode 100644
index 0000000000000000000000000000000000000000..ea4471589cc04d6929091ac3fc92ec3a88513a85
--- /dev/null
+++ b/scripts/ih-flood-fill
@@ -0,0 +1,42 @@
+#!python
+import argparse
+import traceback
+import ih.imgproc
+
+parser = argparse.ArgumentParser(description = "Smoothes an image based on a evenly distributed kernel.")
+parser.add_argument("--input", dest="input", help="Path to input image.", required = True)
+parser.add_argument("--mask", dest="mask", help="Path to mask image.", required = True)
+parser.add_argument("--low", dest="low", nargs="+", type=int, help="Maximal lower brigthness/color difference.", required = True)
+parser.add_argument("--high", dest="high", nargs="+", type=int, help="Maximal upper brigthness/color difference.", required = True)
+parser.add_argument("--writeColor", dest="writeColor", nargs="+", type=int, help="Write Color.")
+parser.add_argument("--connectivity", dest="connectivity", type=int, default=4, help="Number of neighboring pixels to consider.")
+parser.add_argument("--fixed", dest="fixed", default=False, action="store_true", help="Use difference relative to the seed.")
+parser.add_argument("--seedx", dest="seedx", type=int, default=0, help="X coordinate of the seed.")
+parser.add_argument("--seedy", dest="seedy", type=int, default=0, help="Y coordinate of the seed.")
+parser.add_argument("--findSeed", dest="findSeed", default=False, action="store_true", help="Calculate seed from a given image.")
+parser.add_argument("--seedMask", dest="seedMask", help="Path to seed mask image.")
+parser.add_argument("--binary", dest="binary", default=False, action="store_true", help="Specify if flood is performed on a grayscale image.")
+parser.add_argument("--outputdir", dest="outputdir", default=".", help="Path to write output files, if not specified use current directory.")
+parser.add_argument("--output", default=None, dest="output", help="Name of output image to write, if not specified, use input image name.")
+parser.add_argument("--writeblank", default=False, action="store_true", help="If errors happen, write a blank file. Used to ensure dependent files exist for pegasus workflows.")
+args = parser.parse_args()
+
+try:
+ plant = ih.imgproc.Image(args.input, args.outputdir, args.output, False)
+ plant.floodFill(args.mask,
+ tuple(args.low),
+ tuple(args.high),
+ writeColor = tuple(args.writeColor),
+ connectivity = args.connectivity,
+ fixed = args.fixed,
+ seed = tuple([args.seedx, args.seedy]),
+ findSeed = args.findSeed,
+ seedMask = args.seedMask,
+ binary = args.binary
+ )
+ plant.write()
+except Exception as e:
+ print traceback.format_exc()
+ if args.writeblank:
+ with open(args.outputdir + "/" + args.output, "w") as wh:
+ wh.write("not an image.")
diff --git a/scripts/ih-split b/scripts/ih-split
new file mode 100644
index 0000000000000000000000000000000000000000..6b12d0e475c3a4074fcfa748fce6687cd6a8f3d9
--- /dev/null
+++ b/scripts/ih-split
@@ -0,0 +1,22 @@
+#!python
+import argparse
+import traceback
+import ih.imgproc
+
+parser = argparse.ArgumentParser(description = "Splits an image into channels and extracts a single one.")
+parser.add_argument("--input", dest="input", help="Path to input image.", required = True)
+parser.add_argument("--channel", dest="channel", type=int, help="Channel to extract.", required = True)
+parser.add_argument("--outputdir", dest="outputdir", default=".", help="Path to write output files, if not specified use current directory.")
+parser.add_argument("--output", default=None, dest="output", help="Name of output image to write, if not specified, use input image name.")
+parser.add_argument("--writeblank", default=False, action="store_true", help="If errors happen, write a blank file. Used to ensure dependent files exist for pegasus workflows.")
+args = parser.parse_args()
+
+try:
+ plant = ih.imgproc.Image(args.input, args.outputdir, args.output, False)
+ plant.split(args.channel)
+ plant.write()
+except Exception as e:
+ print traceback.format_exc()
+ if args.writeblank:
+ with open(args.outputdir + "/" + args.output, "w") as wh:
+ wh.write("not an image.")
diff --git a/setup.py b/setup.py
index f3fe22ed674e6ceb686504c9ddb9e41ea088e132..7058356d589b682d424dd16ef39e94408cdd0533 100755
--- a/setup.py
+++ b/setup.py
@@ -29,6 +29,9 @@ setup(
"scripts/ih-resize",
"scripts/ih-mask",
"scripts/ih-add-weighted",
+ "scripts/ih-split",
+ "scripts/ih-equalize-hist",
+ "scripts/ih-flood-fill",
"scripts/ih-setup",
"scripts/ih-crawl",