Commit 5490c4f4 authored by Istvan N Huszar's avatar Istvan N Huszar
Browse files

Mouse optimised version 1

parent 853dc941
......@@ -166,8 +166,8 @@
"opt_step": 0.1,
"optsize": 8,
"regweight": 0,
"slice_scaling": [1, 1],
"slice_smoothing": [1, 0],
"slice_scaling": [1],
"slice_smoothing": [0],
"support": {
"mask": {
"automask": {
......@@ -185,8 +185,8 @@
"upper_dz": 0.5,
"vectorder": "xyz",
"visualise": false,
"volume_scaling": [1, 1],
"volume_smoothing": [1, 0],
"volume_scaling": [1],
"volume_smoothing": [0],
"xtol_abs": 0.01
},
"stage_5": {
......@@ -215,7 +215,7 @@
"pages": [3],
"mask": {
"automask": {
"thr": 0.001,
"thr": 0.0,
"uthr": 1.0
},
"file": null,
......
......@@ -1428,8 +1428,10 @@ def stage3(img, vol, cnf):
logger.info(f"Smoothing: ssc={ssc}, ssm={ssm}px, vsc={vsc}, "
f"vsm={vsm}vx.")
img.rescale(1. / ssc, copy=False)
img.storage = MEM
img_smooth = img.smooth(ssm, copy=True)
vol.rescale(1. / vsc, copy=False)
vol.storage = MEM
if vsm != 0:
vol_smooth = vol.smooth(vsm, copy=True)
else:
......@@ -1601,8 +1603,10 @@ def stage4(img, vol, cnf):
logger.info(f"Smoothing: ssc={ssc}, ssm={ssm}px, vsc={vsc}, "
f"vsm={vsm}vx.")
img.rescale(1. / ssc, copy=False)
img.storage = MEM
img_smooth = img.smooth(ssm, copy=True)
vol.rescale(1. / vsc, copy=False)
vol.storage = MEM
if vsm != 0:
vol_smooth = vol.smooth(vsm, copy=True)
else:
......
......@@ -164,6 +164,7 @@ def load_histology(**imageinputmodule):
if qfile.endswith((ts.EXTENSIONS["TImage"],
ts.EXTENSIONS["TIRLObject"])):
img = load_timage(q.file)
img.storage = q.storage
logger.info(f"Loaded histology image from {q.file}: {img}")
return img
......@@ -256,6 +257,7 @@ def load_image(**imageinputmodule):
if q.file.lower().endswith(
(ts.EXTENSIONS["TImage"], ts.EXTENSIONS["TIRLObject"])):
img = load_timage(q.file)
img.storage = q.storage
logger.info(f"Loaded image from {q.file}: {img}")
return img
......
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