# HG changeset patch
# User imgteam
# Date 1553526876 14400
# Node ID 37a75bac5b72b6a5a33aedb82d7aff0ad06f0a08
# Parent ca46066e9768e1c77f10f394f7b66209dc180b66
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/coordinates_of_roi/ commit da043bdec956714abb0fa82f278931bbe1a6d41d
diff -r ca46066e9768 -r 37a75bac5b72 coordinates_of_roi.py
--- a/coordinates_of_roi.py Wed Mar 20 09:17:21 2019 -0400
+++ b/coordinates_of_roi.py Mon Mar 25 11:14:36 2019 -0400
@@ -14,7 +14,7 @@
img_width = data.shape[1]
for j in range(img_width):
for i in range(img_height):
- if white_obj == False:
+ if white_obj == False:
if data[i,j] <= threshold:
x.append(i + offset[0])
y.append(j + offset[1])
@@ -31,12 +31,10 @@
parser = argparse.ArgumentParser(description = "Create a csv table with Coordinates of the ROI")
parser.add_argument("im", help = "Paste path to out.png (output created by transformation)")
parser.add_argument("pixel_table", help = "Paste path to file in which list with all pixles > threshold should be saved")
- parser.add_argument('offset_x', type=int, help='offset in x direction (width)', default=0)
- parser.add_argument('offset_y', type=int, help='offset in y direction (height)', default=0)
parser.add_argument("--white_obj", dest = "white_obj", default=False, help = "If set objects in image are white otherwise black", action = "store_true")
parser.add_argument("--threshold", dest = "threshold", default = 0.5, help = "Enter desired threshold value", type = float)
args = parser.parse_args()
# with warnings.catch_warnings():
# warnings.simplefilter("ignore")
- get_pixel_values(args.im, args.pixel_table, args.white_obj, args.threshold, [args.offset_x, args.offset_y])
+ get_pixel_values(args.im, args.pixel_table, args.white_obj, args.threshold)
diff -r ca46066e9768 -r 37a75bac5b72 coordinates_of_roi.xml
--- a/coordinates_of_roi.xml Wed Mar 20 09:17:21 2019 -0400
+++ b/coordinates_of_roi.xml Mon Mar 25 11:14:36 2019 -0400
@@ -9,7 +9,6 @@
python '$__tool_directory__/coordinates_of_roi.py'
'$im'
'$pixel_table'
- $offset_x $offset_y
$white_obj
--threshold $threshold
]]>
@@ -19,8 +18,6 @@
-
-
@@ -31,13 +28,6 @@
-
-
-
-
-
-
-
**What it does**