Commit d27b5b23 authored by aknecht2's avatar aknecht2
Browse files

Fixed height calculation for dimFromROI. Added output for blecha workflow.

parent 43cbafc8
...@@ -11,7 +11,7 @@ ...@@ -11,7 +11,7 @@
{ {
"name": "crop_center", "name": "crop_center",
"executable": "ih-crop", "executable": "ih-crop",
"inputs": ["normal", "rgbtv_center.json"], "inputs": ["normal", "/home/aknecht/stash/walia/ih/workflows/blecha/input/rgbtv_center.json"],
"outputs": ["centeronly"], "outputs": ["centeronly"],
"arguments": {}, "arguments": {},
"depends": ["normalize"] "depends": ["normalize"]
...@@ -54,7 +54,7 @@ ...@@ -54,7 +54,7 @@
"--weight1": 1.5, "--weight1": 1.5,
"--weight2": -0.5 "--weight2": -0.5
}, },
"depends": ["blur"] "depends": ["blur", "normalize"]
}, },
{ {
"name": "extract_green", "name": "extract_green",
...@@ -100,10 +100,10 @@ ...@@ -100,10 +100,10 @@
"arguments": { "arguments": {
"--low": "50", "--low": "50",
"--high": "50", "--high": "50",
"--writecolor": "255",
"--connectivity": 8, "--connectivity": 8,
"--findSeed": "", "--findSeed": "",
"--binary": "" "--binary": "",
"--writeColor": "255"
}, },
"depends": ["equalize", "bgmask", "create_seed_mask"] "depends": ["equalize", "bgmask", "create_seed_mask"]
}, },
...@@ -121,10 +121,10 @@ ...@@ -121,10 +121,10 @@
{ {
"name": "combine_with_mask", "name": "combine_with_mask",
"executable": "ih-bitwise-or", "executable": "ih-bitwise-or",
"inputs": ["flood_binary", "bgmask"], "inputs": ["flood_binary", "bg_mask"],
"outputs": ["invmask"], "outputs": ["invmask"],
"arguments": {}, "arguments": {},
"depends": ["thresh"] "depends": ["thresh", "bgmask"]
}, },
{ {
"name": "invert", "name": "invert",
...@@ -137,7 +137,8 @@ ...@@ -137,7 +137,8 @@
{ {
"name": "crop_edges", "name": "crop_edges",
"executable": "ih-crop", "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"], "outputs": ["edged_mask"],
"depends": ["invert"] "depends": ["invert"]
}, },
...@@ -249,7 +250,7 @@ ...@@ -249,7 +250,7 @@
{ {
"name": "crop", "name": "crop",
"executable": "ih-crop", "executable": "ih-crop",
"inputs": ["bfiltered", "rgbsv_edge.json"], "inputs": ["bfiltered", "/home/aknecht/stash/walia/ih/workflows/blecha/input/rgbsv_edge.json"],
"outputs": ["edged"], "outputs": ["edged"],
"arguments": {}, "arguments": {},
"depends": ["box_filter"] "depends": ["box_filter"]
...@@ -265,7 +266,7 @@ ...@@ -265,7 +266,7 @@
{ {
"name": "reconstitute", "name": "reconstitute",
"executable": "ih-bitwise-and", "executable": "ih-bitwise-and",
"inputs": ["fmask"], "inputs": ["fmask", "base"],
"outputs": ["recolor"], "outputs": ["recolor"],
"arguments": {}, "arguments": {},
"depends": ["mask"] "depends": ["mask"]
...@@ -284,13 +285,13 @@ ...@@ -284,13 +285,13 @@
] ]
}, },
"options": { "options": {
"save-steps": "true"
}, },
"extract": { "extract": {
"histogram-bin": { "histogram-bin": {
"--group": {"rgb": ["rgbsv", "rgbtv"], "fluo": ["fluosv"]}, "--group": {"rgb": ["rgbsv", "rgbtv"]},
"--chunks": {"rgb": [5, 5, 5], "fluo": [0, 9, 10]}, "--chunks": {"rgb": [5, 5, 5]},
"--channels": {"rgb": [0, 1, 2], "fluo": [1, 2]} "--channels": {"rgb": [0, 1, 2]}
}, },
"workflows": { "workflows": {
"rgbsv": { "rgbsv": {
......
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\ No newline at end of file
...@@ -1246,11 +1246,12 @@ class Image(object): ...@@ -1246,11 +1246,12 @@ class Image(object):
pot = self._loadROI(roi) pot = self._loadROI(roi)
plant = self.getBounds() plant = self.getBounds()
height = plant[0] - pot[0] height = pot[0] - plant[0]
width = plant[3] - plant[2]
if self.conn: if self.conn:
self._addColumn("height") self._addColumn("height")
self._addColumn("width") 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() self.conn.commit()
return return
else: else:
......
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