From a51ca33e26389c822eeea73a6c57dda889943905 Mon Sep 17 00:00:00 2001
From: lpbsscientist <lpbsscientist@gmail.com>
Date: Fri, 13 Aug 2021 23:23:08 +0200
Subject: [PATCH] SJR: latest
---
GUI_main.py | 7 ++++++-
init/InitButtons.py | 2 ++
unet/neural_network.py | 12 ++++++++++--
unet/segment.py | 26 ++++++++++++++++++++++----
4 files changed, 40 insertions(+), 7 deletions(-)
diff --git a/GUI_main.py b/GUI_main.py
index 1dbc1f8..a571ac1 100644
--- a/GUI_main.py
+++ b/GUI_main.py
@@ -1257,6 +1257,10 @@ class App(QMainWindow):
if do_draw or do_erase:
self.m.tempmask = self.m.plotmask.copy()
+ #save status of the showval check box, then turn off (slows brush/eraser down too much)
+ self.showval_was_checked = self.button_showval.isChecked()
+ self.button_showval.setChecked(False)
+
if do_draw:
self.WriteStatusBar(('Draw using the brush, right click to select '
'the cell to draw.'))
@@ -1271,7 +1275,7 @@ class App(QMainWindow):
self.id2 = self.m.mpl_connect('button_press_event',
lambda e: self.m.OneClick(e, radius))
self.id = self.m.mpl_connect('motion_notify_event',
- lambda e: self.m.PaintBrush(e, radius))
+ lambda e: self.m.PaintBrush(e, radius))
self.id3 = self.m.mpl_connect('button_release_event', self.m.ReleaseClick)
@@ -1282,6 +1286,7 @@ class App(QMainWindow):
QApplication.restoreOverrideCursor()
self.Enable(self.button_drawmouse)
self.Enable(self.button_eraser)
+ self.button_showval.setChecked(self.showval_was_checked)
self.SaveMask()
self.ClearStatusBar()
diff --git a/init/InitButtons.py b/init/InitButtons.py
index 3dff210..60ab866 100644
--- a/init/InitButtons.py
+++ b/init/InitButtons.py
@@ -158,6 +158,8 @@ def Init(parent):
parent.button_changecellvalue.setEnabled(True)
parent.button_changecellvalue.clicked.connect(parent.ChangeOneValue)
parent.button_changecellvalue.setMaximumWidth(150)
+ parent.button_changecellvalue.setShortcut("C")
+ parent.button_changecellvalue.setToolTip("Shortcut: C")
# parent.button_changecellvalue.setStatusTip('')
parent.button_changecellvalue.setStatusTip('Change ID value of one cell. Use left click to select one cell and enter a new ID value.')
diff --git a/unet/neural_network.py b/unet/neural_network.py
index c3e66a6..543af68 100644
--- a/unet/neural_network.py
+++ b/unet/neural_network.py
@@ -65,9 +65,17 @@ def prediction(im, is_pc):
input_size = (None,None,1))
if is_pc:
- path = path_weights + 'unet_weights_batchsize_25_Nepochs_100_SJR0_10.hdf5'
+ path = '/home/sjrahi/Research/YeaZ/unet_weights/2021_05_27_budding_BF_all/files-p-G/unet_weights_budding_BF_multilab-p-G_SJR_0_1_batchsize_10_Nepochs_250.hdf5'
+ # '/home/sjrahi/Research/YeaZ/unet_weights/2021_04_15_Silke_pombe/unet_weights_pombe_Silke_all_SJR_0_1_batchsize_5_Nepochs_500.hdf5'
+ # path_weights + 'unet_weights_batchsize_25_Nepochs_100_SJR0_10.hdf5'
else:
- path = path_weights + 'weights_budding_BF_02.hdf5'
+ path = '/home/sjrahi/Research/YeaZ/unet_weights/2021_05_09_pombe_all/unet_weights_pombe_all_SJR_0_2_batchsize_8_Nepochs_400.hdf5'
+ # '/home/sjrahi/Research/YeaZ/unet_weights/2021_04_15_Silke_pombe/unet_weights_BF_batchsize_15_Nepochs_400_SJR_0_1.hdf5'
+ # '/home/sjrahi/Research/YeaZ/unet_weights/2021_04_15_Silke_pombe/unet_weights_BF_batchsize_25_Nepochs_200_SJR_0_1.hdf5'
+ # '/home/sjrahi/Research/YeaZ/unet_weights/2021_04_15_Silke_pombe/unet_weights_epoch_600_batchsize_50_fold_1_4.hdf5'
+ # '/home/sjrahi/Research/YeaZ/unet_weights/2021_04_15_Silke_pombe/unet_weights_epoch_2000_batchsize_50_fold_1.hdf5'
+ # '/home/sjrahi/Research/YeaZ/unet_weights/2021_04_15_Silke_pombe/unet_weights_epoch_600_batchsize_50_fold_1_4.hdf5'
+ # path_weights + 'weights_budding_BF_02.hdf5'
if not os.path.exists(path):
raise ValueError('Path does not exist')
diff --git a/unet/segment.py b/unet/segment.py
index 2a7822e..c333fb9 100644
--- a/unet/segment.py
+++ b/unet/segment.py
@@ -94,10 +94,12 @@ def cell_merge(wsh, pred):
objcounter = objcounter + 1
orig1 = objs[obj1,:,:]
+
+ last_obj2_added_to_obj1 = -1
for obj2 in range(obj1+1,wsh.max()):
dil2 = dil_objs[obj2,:,:]
-
+
# only check border if bounding box overlaps, and second mask
# is not yet deleted
if (do_box_overlap(obj_coords[obj1,:], obj_coords[obj2,:])
@@ -107,7 +109,7 @@ def cell_merge(wsh, pred):
border_pred = pred[border]
# Border is too small to be considered
- if len(border_pred) < 32:
+ if len(border_pred) < 16: #SJR: Changed on 18.04.2021 from previously 32. Not sure why 32. I remember 8.
continue
# Sum of top 25% of predicted border values
@@ -119,11 +121,27 @@ def cell_merge(wsh, pred):
# merge cells
if top_border_height / top_border_area > .99:
orig1 = np.logical_or(orig1, objs[obj2,:,:])
- dil_objs[obj1,:,:] = np.logical_or(dil1, dil2)
+ dil1 = np.logical_or(dil1, dil2)
+ dil_objs[obj1,:,:] = dil1
dil_objs[obj2,:,:] = np.zeros((wshshape[0], wshshape[1]))
obj_coords[obj1,:] = get_bounding_box(dil_objs[obj1,:,:])
+# obj_coords[obj2,:] = get_bounding_box(dil_objs[obj2,:,:])
+ last_obj2_added_to_obj1 = obj2
+
+ # the last object that obj1 was merged with should be equal to obj1 so that additional cells could be merged with it
+ if last_obj2_added_to_obj1 > -1:
+ obj2 = last_obj2_added_to_obj1
+ dil_objs[obj2,:,:] = dil1
+ objs[obj2,:,:] = orig1
+ obj_coords[obj2,:] = get_bounding_box(dil_objs[obj2,:,:])
+
- wshclean = wshclean + orig1*objcounter
+ wshclean = (1-orig1)*wshclean + orig1*objcounter
+
+ # resort wshclean
+ u = np.unique(wshclean)[1:] #ignore background
+ for obj1 in range(len(u)):
+ wshclean[wshclean==u[obj1]] = obj1 + 1
return wshclean
--
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