fix bug for roi manager

.gitignore

@@ -1,3 +1,4 @@
+imagepy/data/config.json
 # Byte-compiled / optimized / DLL files
 __pycache__/
 *.py[cod]

imagepy/data/config.json

@@ -1 +1 @@
-[["uistyle", "imagepy", null], ["mea_style", {"color": [0, 0, 255], "fcolor": [255, 255, 255], "fill": false, "lw": 2, "tcolor": [0, 255, 0], "size": 12}, null], ["mark_style", {"color": [0, 255, 0], "fcolor": [255, 255, 255], "fill": false, "lw": 1, "tcolor": [255, 0, 0], "size": 8}, null], ["recent", ["C:/Users/54631/Desktop/\u6d77\u51b0\u62a5\u4ef7/testmacros.mc", "C:\\Users\\Administrator\\Downloads\\\u7d20\u6750\u2014\u8f66\u5934\\\u6d4b\u8bd5-JK1-\u52ff\u5220\\20170201\\In-20170201151126911-\u6842J73220-\u9ec4-qj-1.jpg", "C:/Users/Administrator/Desktop/imagepy/imagepy/plugins/demoplugin/menus/Demos/Macros Demo/Macros Gaussian Invert.mc", "DEM.mc"], null], ["roi_style", {"color": [255, 255, 0], "fcolor": [255, 255, 255], "fill": false, "lw": 1, "tcolor": [255, 255, 0], "size": 8}, null], ["language", "English", null]]
+[["language", "English", null], ["roi_style", {"color": [255, 255, 0], "fcolor": [255, 255, 255], "fill": false, "lw": 1, "tcolor": [255, 255, 0], "size": 8}, null], ["recent", ["C:/Users/54631/Desktop/\u6d77\u51b0\u62a5\u4ef7/testmacros.mc", "C:\\Users\\Administrator\\Downloads\\\u7d20\u6750\u2014\u8f66\u5934\\\u6d4b\u8bd5-JK1-\u52ff\u5220\\20170201\\In-20170201151126911-\u6842J73220-\u9ec4-qj-1.jpg", "C:/Users/Administrator/Desktop/imagepy/imagepy/plugins/demoplugin/menus/Demos/Macros Demo/Macros Gaussian Invert.mc", "DEM.mc"], null], ["mark_style", {"color": [0, 255, 0], "fcolor": [255, 255, 255], "fill": false, "lw": 1, "tcolor": [255, 0, 0], "size": 8}, null], ["mea_style", {"color": [0, 0, 255], "fcolor": [255, 255, 255], "fill": false, "lw": 2, "tcolor": [0, 255, 0], "size": 12}, null], ["uistyle", "imagepy", null]]

imagepy/menus/Kit3D/Analysis 3D/regionprops3d_plgs.py

@@ -1,7 +1,8 @@
 import numpy as np
 from sciapp.action import Simple, Filter
 from scipy.ndimage import label, generate_binary_structure
-from skimage.measure import marching_cubes_lewiner, mesh_surface_area
+# from skimage.measure import marching_cubes_lewiner, mesh_surface_area # scikit-image 0.15
+from skimage.measure import marching_cubes, mesh_surface_area # scikit-image 0.19
 from skimage.segmentation import find_boundaries
 from skimage.measure import regionprops
 from numpy.linalg import norm
@@ -65,7 +66,8 @@ def run(self, ips, imgs, para = None):
             dt.append([round(i.centroid[2]*k,1) for i in ls])
         if para['surf']:
             buf[find_boundaries(buf, mode='outer')] = 0
-            vts, fs, ns, cs = marching_cubes_lewiner(buf, level=0)
+            # vts, fs, ns, cs = marching_cubes_lewiner(buf, level=0) # scikit-image 0.15
+            vts, fs, ns, cs = marching_cubes(buf, level=0, method='lewiner') # scikit-image 0.19
             lst = [[] for i in range(n+1)]
             for i in fs: lst[int(cs[i[0]])].append(i)
             dt.append([0 if len(i)==0 else mesh_surface_area(vts, np.array(i))*k**2 for i in lst][1:])
@@ -124,4 +126,4 @@ def run(self, ips, imgs, para = None):
         idx[0] = para['front'] if para['inv'] else 0
         imgs[:] = idx[lab]
 
-plgs = [RegionLabel, RegionCounter, RegionFilter]
+plgs = [RegionLabel, RegionCounter, RegionFilter]

imagepy/menus/Kit3D/Analysis 3D/surfacemeasure_plg.py

@@ -1,5 +1,6 @@
 from sciapp.action import Filter
-from skimage.measure import marching_cubes_lewiner, mesh_surface_area
+from skimage.measure import marching_cubes, mesh_surface_area
+# from skimage.measure import marching_cubes_lewiner, mesh_surface_area
 import numpy as np
 import pandas as pd
 
@@ -37,8 +38,9 @@ def run(self, ips, snap, img, para = None):
         sfront = (ips.imgs[::ds,::ds,::ds]>lev).sum() * ds ** 3 * k**3
         sback = scube - sfront
         print(scube, sfront, sback)
-        vts, fs, ns, cs =  marching_cubes_lewiner(ips.imgs[::ds,::ds,::ds], lev, step_size=step)
+        # vts, fs, ns, cs =  marching_cubes_lewiner(ips.imgs[::ds,::ds,::ds], lev, step_size=step)
+        vts, fs, ns, cs =  marching_cubes(ips.imgs[::ds,::ds,::ds], lev, step_size=step, method='lewiner')
         area = mesh_surface_area(vts, fs) * (ds**2 * k **2)
         rst = [round(i,3) for i in [scube, sfront, sback, sfront/scube, area, area/sfront]]
         titles = ['Cube Volume', 'Volume', 'Blank', 'Volume/Cube', 'Surface', 'Volume/Surface']
-        IPy.show_table(pd.DataFrame([rst], columns=titles), ips.title+'-Volume Measure')
+        IPy.show_table(pd.DataFrame([rst], columns=titles), ips.title+'-Volume Measure')

imagepy/menus/Selection/roiwindow_wgt.py

@@ -232,7 +232,7 @@ def on_add(self, event):
 		Macros('', ['ROI Add>None']).start(self.app, callafter=self.UpdateData)
 
 	def on_add_nameless(self, event):
-		ips = ImageManager.get()
+		ips = self.app.get_img()
 		if ips is None: return self.app.alert('No image opened!')
 		if ips.roi is None: return self.app.alert('No Roi found!')
 		Macros('', ['ROI Add>{"name":"%s-roi"}'%ips.title]).start(self.app, callafter=self.UpdateData)
@@ -313,10 +313,14 @@ def on_setting(self, event):
 		Macros('', ['ROI Setting>None']).start(self.app)
 
 	def UpdateData(self):
-		names = self.app.manager('roi').gets('name')
-		objs = self.app.manager('roi').gets('obj')
-		types = [ROI(mark2shp(i)).roitype for i in objs]
+		names = self.app.manager('roi').names()
+		if len(names) == 0:
+			objs = []
+		else:
+			objs = self.app.manager('roi').gets()
+		types = [ROI(mark2shp(i[1])).roitype for i in objs]
 		self.lst_rois.SetValue(list(zip(names, types)))
+		self.lst_rois.Refresh()
 
 	def __del__( self ):
 		pass

imagepy/tools/Draw/aibrush_tol.py

@@ -2,7 +2,8 @@
 import numpy as np
 from time import time
 from skimage.morphology import flood_fill, flood
-from skimage.draw import line, circle
+# from skimage.draw import line, circle
+from skimage.draw import line, disk
 from skimage.segmentation import felzenszwalb
 from sciapp.util import mark2shp
 from scipy.ndimage import binary_fill_holes, binary_dilation, binary_erosion
@@ -21,15 +22,17 @@ def local_brush(img, back, r, c, color, sigma, msize):
 
 def local_pen(img, r, c, R, color):
     img = img.reshape((img.shape+(1,))[:3])
-    rs, cs = circle(r, c, R/2+1e-6, shape=img.shape)
+    # rs, cs = circle(r, c, R/2+1e-6, shape=img.shape)
+    rs, cs = disk((r, c), R/2+1e-6, shape=img.shape)
     img[rs, cs] = color
 
 def local_in_fill(img, r, c, R, color, bcolor):
     img = img.reshape((img.shape+(1,))[:3])
     msk = (img == color).min(axis=2)
     filled = binary_fill_holes(msk)
     filled ^= msk
-    rs, cs = circle(r, c, R/2+1e-6, shape=img.shape)
+    # rs, cs = circle(r, c, R/2+1e-6, shape=img.shape)
+    rs, cs = disk((r, c), R/2+1e-6, shape=img.shape)
     msk[:] = 0
     msk[rs, cs] = 1
     msk &= filled
@@ -38,7 +41,8 @@ def local_in_fill(img, r, c, R, color, bcolor):
 def local_out_fill(img, r, c, R, color, bcolor):
     img = img.reshape((img.shape+(1,))[:3])
     msk = (img != color).max(axis=2)
-    rs, cs = circle(r, c, R/2+1e-6, shape=img.shape)
+    # rs, cs = circle(r, c, R/2+1e-6, shape=img.shape)
+    rs, cs = disk((r, c), R/2+1e-6, shape=img.shape)
     buf = np.zeros_like(msk)
     buf[rs, cs] = 1
     msk &= buf
@@ -49,7 +53,8 @@ def local_sketch(img, r, c, R, color, bcolor):
     msk = (img == color).min(axis=2)
     dilation = binary_dilation(msk, np.ones((3,3)))
     dilation ^= msk
-    rs, cs = circle(r, c, R/2+1e-6, shape=img.shape)
+    # rs, cs = circle(r, c, R/2+1e-6, shape=img.shape)
+    rs, cs = disk((r, c), R/2+1e-6, shape=img.shape)
     msk[:] = 0
     msk[rs, cs] = 1
     msk &= dilation
@@ -280,4 +285,4 @@ def mouse_wheel(self, ips, x, y, d, **key):
         elif self.status == None:
             if d>0:key['canvas'].zoomout(x, y, 'data')
             if d<0:key['canvas'].zoomin(x, y, 'data')
-        ips.update()
+        ips.update()

imagepy/tools/Standard/painter_tol.py

@@ -1,10 +1,12 @@
 from sciapp.action import ImageTool
-from skimage.draw import line, circle
+# from skimage.draw import line, circle
+from skimage.draw import line, disk 
 
 def drawline(img, oldp, newp, w, value):
     if img.ndim == 2 and hasattr(value, '__iter__'): value = sum(value)/3
     oy, ox = line(*[int(round(i)) for i in oldp+newp])
-    cy, cx = circle(0, 0, w/2+1e-6)
+    # cy, cx = circle(0, 0, w/2+1e-6)
+    cy, cx = disk((0, 0), w/2+1e-6)
     ys = (oy.reshape((-1,1))+cy).clip(0, img.shape[0]-1)
     xs = (ox.reshape((-1,1))+cx).clip(0, img.shape[1]-1)
     img[ys.ravel(), xs.ravel()] = value
@@ -35,4 +37,4 @@ def mouse_move(self, ips, x, y, btn, **key):
         self.oldp = (y, x)
         ips.update()
 
-    def mouse_wheel(self, ips, x, y, d, **key):pass
+    def mouse_wheel(self, ips, x, y, d, **key):pass

requirements.txt

@@ -15,3 +15,6 @@ markdown
 python-markdown-math
 moderngl
 dulwich
+matplotlib
+vispy
+pystackreg