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Image Harvest
Commit d27b5b23 authored by aknecht2's avatar aknecht2
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Fixed height calculation for dimFromROI. Added output for blecha workflow.

parent 43cbafc8
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Showing with 12598 additions and 15 deletions
examples/workflows/blecha/imgproc.json
View file @ d27b5b23
......@@ -11,7 +11,7 @@
{
"name": "crop_center",
"executable": "ih-crop",
"inputs": ["normal", "rgbtv_center.json"],
"inputs": ["normal", "/home/aknecht/stash/walia/ih/workflows/blecha/input/rgbtv_center.json"],
"outputs": ["centeronly"],
"arguments": {},
"depends": ["normalize"]
......@@ -54,7 +54,7 @@
"--weight1": 1.5,
"--weight2": -0.5
},
"depends": ["blur"]
"depends": ["blur", "normalize"]
},
{
"name": "extract_green",
......@@ -100,10 +100,10 @@
"arguments": {
"--low": "50",
"--high": "50",
"--writecolor": "255",
"--connectivity": 8,
"--findSeed": "",
"--binary": ""
"--binary": "",
"--writeColor": "255"
},
"depends": ["equalize", "bgmask", "create_seed_mask"]
},
......@@ -121,10 +121,10 @@
{
"name": "combine_with_mask",
"executable": "ih-bitwise-or",
"inputs": ["flood_binary", "bgmask"],
"inputs": ["flood_binary", "bg_mask"],
"outputs": ["invmask"],
"arguments": {},
"depends": ["thresh"]
"depends": ["thresh", "bgmask"]
},
{
"name": "invert",
......@@ -137,7 +137,8 @@
{
"name": "crop_edges",
"executable": "ih-crop",
"inputs": ["premask", "rgbtv_edge.json"],
"inputs": ["premask", "/home/aknecht/stash/walia/ih/workflows/blecha/input/rgbtv_edge.json"],
"arguments": {},
"outputs": ["edged_mask"],
"depends": ["invert"]
},
......@@ -249,7 +250,7 @@
{
"name": "crop",
"executable": "ih-crop",
"inputs": ["bfiltered", "rgbsv_edge.json"],
"inputs": ["bfiltered", "/home/aknecht/stash/walia/ih/workflows/blecha/input/rgbsv_edge.json"],
"outputs": ["edged"],
"arguments": {},
"depends": ["box_filter"]
......@@ -265,7 +266,7 @@
{
"name": "reconstitute",
"executable": "ih-bitwise-and",
"inputs": ["fmask"],
"inputs": ["fmask", "base"],
"outputs": ["recolor"],
"arguments": {},
"depends": ["mask"]
......@@ -284,13 +285,13 @@
]
},
"options": {
"save-steps": "true"
},
"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]}
"--group": {"rgb": ["rgbsv", "rgbtv"]},
"--chunks": {"rgb": [5, 5, 5]},
"--channels": {"rgb": [0, 1, 2]}
},
"workflows": {
"rgbsv": {
......
examples/workflows/blecha/output/images.csv 0 → 100644
View file @ d27b5b23
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examples/workflows/blecha/output/imgproc.log 0 → 100644
View file @ d27b5b23
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examples/workflows/blecha/output/rgb_hist_bins.json 0 → 100644
View file @ d27b5b23
[{"max": [27, 43, 38], "name": "rgb_bin1", "min": [1, 1, 1]}, {"max": [27, 43, 48], "name": "rgb_bin2", "min": [1, 1, 38]}, {"max": [27, 43, 58], "name": "rgb_bin3", "min": [1, 1, 48]}, {"max": [27, 43, 79], "name": "rgb_bin4", "min": [1, 1, 58]}, {"max": [27, 43, 255], "name": "rgb_bin5", "min": [1, 1, 79]}, {"max": [27, 53, 38], "name": "rgb_bin6", "min": [1, 43, 1]}, {"max": [27, 53, 48], "name": "rgb_bin7", "min": [1, 43, 38]}, {"max": [27, 53, 58], "name": "rgb_bin8", "min": [1, 43, 48]}, {"max": [27, 53, 79], "name": "rgb_bin9", "min": [1, 43, 58]}, {"max": [27, 53, 255], "name": "rgb_bin10", "min": [1, 43, 79]}, {"max": [27, 63, 38], "name": "rgb_bin11", "min": [1, 53, 1]}, {"max": [27, 63, 48], "name": "rgb_bin12", "min": [1, 53, 38]}, {"max": [27, 63, 58], "name": "rgb_bin13", "min": [1, 53, 48]}, {"max": [27, 63, 79], "name": "rgb_bin14", "min": [1, 53, 58]}, {"max": [27, 63, 255], "name": "rgb_bin15", "min": [1, 53, 79]}, {"max": [27, 87, 38], "name": "rgb_bin16", "min": [1, 63, 1]}, {"max": [27, 87, 48], "name": "rgb_bin17", "min": [1, 63, 38]}, {"max": [27, 87, 58], "name": "rgb_bin18", "min": [1, 63, 48]}, {"max": [27, 87, 79], "name": "rgb_bin19", "min": [1, 63, 58]}, {"max": [27, 87, 255], "name": "rgb_bin20", "min": [1, 63, 79]}, {"max": [27, 255, 38], "name": "rgb_bin21", "min": [1, 87, 1]}, {"max": [27, 255, 48], "name": "rgb_bin22", "min": [1, 87, 38]}, {"max": [27, 255, 58], "name": "rgb_bin23", "min": [1, 87, 48]}, {"max": [27, 255, 79], "name": "rgb_bin24", "min": [1, 87, 58]}, {"max": [27, 255, 255], "name": "rgb_bin25", "min": [1, 87, 79]}, {"max": [35, 43, 38], "name": "rgb_bin26", "min": [27, 1, 1]}, {"max": [35, 43, 48], "name": "rgb_bin27", "min": [27, 1, 38]}, {"max": [35, 43, 58], "name": "rgb_bin28", "min": [27, 1, 48]}, {"max": [35, 43, 79], "name": "rgb_bin29", "min": [27, 1, 58]}, {"max": [35, 43, 255], "name": "rgb_bin30", "min": [27, 1, 79]}, {"max": [35, 53, 38], "name": "rgb_bin31", "min": [27, 43, 1]}, {"max": [35, 53, 48], "name": "rgb_bin32", "min": [27, 43, 38]}, {"max": [35, 53, 58], "name": "rgb_bin33", "min": [27, 43, 48]}, {"max": [35, 53, 79], "name": "rgb_bin34", "min": [27, 43, 58]}, {"max": [35, 53, 255], "name": "rgb_bin35", "min": [27, 43, 79]}, {"max": [35, 63, 38], "name": "rgb_bin36", "min": [27, 53, 1]}, {"max": [35, 63, 48], "name": "rgb_bin37", "min": [27, 53, 38]}, {"max": [35, 63, 58], "name": "rgb_bin38", "min": [27, 53, 48]}, {"max": [35, 63, 79], "name": "rgb_bin39", "min": [27, 53, 58]}, {"max": [35, 63, 255], "name": "rgb_bin40", "min": [27, 53, 79]}, {"max": [35, 87, 38], "name": "rgb_bin41", "min": [27, 63, 1]}, {"max": [35, 87, 48], "name": "rgb_bin42", "min": [27, 63, 38]}, {"max": [35, 87, 58], "name": "rgb_bin43", "min": [27, 63, 48]}, {"max": [35, 87, 79], "name": "rgb_bin44", "min": [27, 63, 58]}, {"max": [35, 87, 255], "name": "rgb_bin45", "min": [27, 63, 79]}, {"max": [35, 255, 38], "name": "rgb_bin46", "min": [27, 87, 1]}, {"max": [35, 255, 48], "name": "rgb_bin47", "min": [27, 87, 38]}, {"max": [35, 255, 58], "name": "rgb_bin48", "min": [27, 87, 48]}, {"max": [35, 255, 79], "name": "rgb_bin49", "min": [27, 87, 58]}, {"max": [35, 255, 255], "name": "rgb_bin50", "min": [27, 87, 79]}, {"max": [48, 43, 38], "name": "rgb_bin51", "min": [35, 1, 1]}, {"max": [48, 43, 48], "name": "rgb_bin52", "min": [35, 1, 38]}, {"max": [48, 43, 58], "name": "rgb_bin53", "min": [35, 1, 48]}, {"max": [48, 43, 79], "name": "rgb_bin54", "min": [35, 1, 58]}, {"max": [48, 43, 255], "name": "rgb_bin55", "min": [35, 1, 79]}, {"max": [48, 53, 38], "name": "rgb_bin56", "min": [35, 43, 1]}, {"max": [48, 53, 48], "name": "rgb_bin57", "min": [35, 43, 38]}, {"max": [48, 53, 58], "name": "rgb_bin58", "min": [35, 43, 48]}, {"max": [48, 53, 79], "name": "rgb_bin59", "min": [35, 43, 58]}, {"max": [48, 53, 255], "name": "rgb_bin60", "min": [35, 43, 79]}, {"max": [48, 63, 38], "name": "rgb_bin61", "min": [35, 53, 1]}, {"max": [48, 63, 48], "name": "rgb_bin62", "min": [35, 53, 38]}, {"max": [48, 63, 58], "name": "rgb_bin63", "min": [35, 53, 48]}, {"max": [48, 63, 79], "name": "rgb_bin64", "min": [35, 53, 58]}, {"max": [48, 63, 255], "name": "rgb_bin65", "min": [35, 53, 79]}, {"max": [48, 87, 38], "name": "rgb_bin66", "min": [35, 63, 1]}, {"max": [48, 87, 48], "name": "rgb_bin67", "min": [35, 63, 38]}, {"max": [48, 87, 58], "name": "rgb_bin68", "min": [35, 63, 48]}, {"max": [48, 87, 79], "name": "rgb_bin69", "min": [35, 63, 58]}, {"max": [48, 87, 255], "name": "rgb_bin70", "min": [35, 63, 79]}, {"max": [48, 255, 38], "name": "rgb_bin71", "min": [35, 87, 1]}, {"max": [48, 255, 48], "name": "rgb_bin72", "min": [35, 87, 38]}, {"max": [48, 255, 58], "name": "rgb_bin73", "min": [35, 87, 48]}, {"max": [48, 255, 79], "name": "rgb_bin74", "min": [35, 87, 58]}, {"max": [48, 255, 255], "name": "rgb_bin75", "min": [35, 87, 79]}, {"max": [79, 43, 38], "name": "rgb_bin76", "min": [48, 1, 1]}, {"max": [79, 43, 48], "name": "rgb_bin77", "min": [48, 1, 38]}, {"max": [79, 43, 58], "name": "rgb_bin78", "min": [48, 1, 48]}, {"max": [79, 43, 79], "name": "rgb_bin79", "min": [48, 1, 58]}, {"max": [79, 43, 255], "name": "rgb_bin80", "min": [48, 1, 79]}, {"max": [79, 53, 38], "name": "rgb_bin81", "min": [48, 43, 1]}, {"max": [79, 53, 48], "name": "rgb_bin82", "min": [48, 43, 38]}, {"max": [79, 53, 58], "name": "rgb_bin83", "min": [48, 43, 48]}, {"max": [79, 53, 79], "name": "rgb_bin84", "min": [48, 43, 58]}, {"max": [79, 53, 255], "name": "rgb_bin85", "min": [48, 43, 79]}, {"max": [79, 63, 38], "name": "rgb_bin86", "min": [48, 53, 1]}, {"max": [79, 63, 48], "name": "rgb_bin87", "min": [48, 53, 38]}, {"max": [79, 63, 58], "name": "rgb_bin88", "min": [48, 53, 48]}, {"max": [79, 63, 79], "name": "rgb_bin89", "min": [48, 53, 58]}, {"max": [79, 63, 255], "name": "rgb_bin90", "min": [48, 53, 79]}, {"max": [79, 87, 38], "name": "rgb_bin91", "min": [48, 63, 1]}, {"max": [79, 87, 48], "name": "rgb_bin92", "min": [48, 63, 38]}, {"max": [79, 87, 58], "name": "rgb_bin93", "min": [48, 63, 48]}, {"max": [79, 87, 79], "name": "rgb_bin94", "min": [48, 63, 58]}, {"max": [79, 87, 255], "name": "rgb_bin95", "min": [48, 63, 79]}, {"max": [79, 255, 38], "name": "rgb_bin96", "min": [48, 87, 1]}, {"max": [79, 255, 48], "name": "rgb_bin97", "min": [48, 87, 38]}, {"max": [79, 255, 58], "name": "rgb_bin98", "min": [48, 87, 48]}, {"max": [79, 255, 79], "name": "rgb_bin99", "min": [48, 87, 58]}, {"max": [79, 255, 255], "name": "rgb_bin100", "min": [48, 87, 79]}, {"max": [255, 43, 38], "name": "rgb_bin101", "min": [79, 1, 1]}, {"max": [255, 43, 48], "name": "rgb_bin102", "min": [79, 1, 38]}, {"max": [255, 43, 58], "name": "rgb_bin103", "min": [79, 1, 48]}, {"max": [255, 43, 79], "name": "rgb_bin104", "min": [79, 1, 58]}, {"max": [255, 43, 255], "name": "rgb_bin105", "min": [79, 1, 79]}, {"max": [255, 53, 38], "name": "rgb_bin106", "min": [79, 43, 1]}, {"max": [255, 53, 48], "name": "rgb_bin107", "min": [79, 43, 38]}, {"max": [255, 53, 58], "name": "rgb_bin108", "min": [79, 43, 48]}, {"max": [255, 53, 79], "name": "rgb_bin109", "min": [79, 43, 58]}, {"max": [255, 53, 255], "name": "rgb_bin110", "min": [79, 43, 79]}, {"max": [255, 63, 38], "name": "rgb_bin111", "min": [79, 53, 1]}, {"max": [255, 63, 48], "name": "rgb_bin112", "min": [79, 53, 38]}, {"max": [255, 63, 58], "name": "rgb_bin113", "min": [79, 53, 48]}, {"max": [255, 63, 79], "name": "rgb_bin114", "min": [79, 53, 58]}, {"max": [255, 63, 255], "name": "rgb_bin115", "min": [79, 53, 79]}, {"max": [255, 87, 38], "name": "rgb_bin116", "min": [79, 63, 1]}, {"max": [255, 87, 48], "name": "rgb_bin117", "min": [79, 63, 38]}, {"max": [255, 87, 58], "name": "rgb_bin118", "min": [79, 63, 48]}, {"max": [255, 87, 79], "name": "rgb_bin119", "min": [79, 63, 58]}, {"max": [255, 87, 255], "name": "rgb_bin120", "min": [79, 63, 79]}, {"max": [255, 255, 38], "name": "rgb_bin121", "min": [79, 87, 1]}, {"max": [255, 255, 48], "name": "rgb_bin122", "min": [79, 87, 38]}, {"max": [255, 255, 58], "name": "rgb_bin123", "min": [79, 87, 48]}, {"max": [255, 255, 79], "name": "rgb_bin124", "min": [79, 87, 58]}, {"max": [255, 255, 255], "name": "rgb_bin125", "min": [79, 87, 79]}]
\ No newline at end of file
ih/imgproc.py
View file @ d27b5b23
......@@ -1246,11 +1246,12 @@ class Image(object):
pot = self._loadROI(roi)
plant = self.getBounds()
height = plant[0] - pot[0]
height = pot[0] - plant[0]
width = plant[3] - plant[2]
if self.conn:
self._addColumn("height")
self._addColumn("width")
self.conn.execute("update images set height=?,width=? where pegasusid=?", (height, self.x, self.dbid))
self.conn.execute("update images set height=?,width=? where pegasusid=?", (height, width, self.dbid))
self.conn.commit()
return
else:
......
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