v0.93

CHANGELOG.md

@@ -29,7 +29,12 @@ directory structures.
 when `python-bioformats` or `javabridge` are not installed.
 16. (v0.92 20230207) Multiple image series in a file is supported but
     only the first one is used. Also imgio has been a lot changed;
-    `tifffile` version had been upgraded and  ome.tif is written out by tifffile.
+    `tifffile` version had been upgraded and  ome.tif is written out
+    by tifffile. Furthermore, with the `nd2` package, nd2 files are
+    directly read without installing bioformats.
+17. (v0.93 20230707) Writing ome.tif is compatible for
+`tifffile` 2021.7.2.
+18. (v0.93 20230709) Bug fix for DeltaVision deconvolved files.
 
 v0.8(May. 2019)
 ----

Chromagnon.spec

@@ -53,21 +53,34 @@ if sys.platform.startswith('win'):
     code=os.path.abspath(os.path.join('Z:', 'py'))
     src = os.path.abspath(os.path.join('Z:', 'src', 'Chromagnon', 'Chromagnon'))
 
-
-    binaries = [(os.path.join(libbin, 'mkl_avx.dll'), '.'), (os.path.join(libbin, 'mkl_avx2.dll'), '.')]
+   # if os.path.isfile(os.path.join(libbin, 'mkl_avx.dll')):
+   #     binaries = [(os.path.join(libbin, 'mkl_avx.dll'), '.')]#, (os.path.join(libbin, 'mkl_avx2.dll'), '.')]
+   # elif os.path.isfile(os.path.join(libbin, 'mkl_avx.2.dll')):
+   #     binaries = [(os.path.join(libbin, 'mkl_avx.2.dll'), '.')]
     if not PLUGIN:
-        if pyversion == 3:
-            glut = 'glut64.dll'
-        elif pyversion == 2:
+        if os.path.isfile(os.path.join(libbin, 'freeglut.dll')):
             glut = os.path.join(libbin, 'freeglut.dll')
+        else:
+            glut = 'glut64.dll'
+        #if pyversion == 3:
+        #    glut = 'glut64.dll'
+        #elif pyversion == 2:
+        #    glut = os.path.join(libbin, 'freeglut.dll')
         binaries += [(os.path.join(home, conda, glut), '.')]
     pylib = 'pyd'
     jvm = 'jvm.dll'
     suffix = 'Win' + ex_suffix
 
 else: # mac + linux
-    code=os.path.join(home, 'codes', 'py')
-    src = os.path.join(home, 'codes', 'src', 'Chromagnon', 'Chromagnon')
+    if os.path.isdir(os.path.expanduser('~/codes/py')):
+        CODE='codes'
+    elif os.path.isdir(os.path.expanduser('~/local/py')):
+        CODE='local'
+    else:
+        raise ValueError('directory for codes not found')
+
+    code=os.path.join(home, CODE, 'py')
+    src = os.path.join(home, CODE, 'src', 'Chromagnon', 'Chromagnon')
 
     site=os.path.join(conda, 'lib', 'python%i.%i' % (pyversion, sys.version_info.minor), 'site-packages')
     print('site is', site)
@@ -104,13 +117,31 @@ else:
     cversion = ''
 # ------- pyinstaller
 
-datas = [(os.path.join(code, 'Priithon', '*.py'), 'Priithon'), (os.path.join(code, 'Priithon', 'plt', '*.py'), os.path.join('Priithon', 'plt')), (os.path.join(code, 'PriCommon', '*.py'), 'PriCommon'), (os.path.join(code, 'common', '*.py'), 'common'), (os.path.join(site, 'tifffile', '*.%s' % pylib), 'tifffile')]
+datas = [(os.path.join(code, 'Priithon', '*.py'), 'Priithon'), (os.path.join(code, 'Priithon', 'plt', '*.py'), os.path.join('Priithon', 'plt')), (os.path.join(code, 'PriCommon', '*.py'), 'PriCommon'), (os.path.join(code, 'common', '*.py'), 'common')]#, (os.path.join(site, 'tifffile', '*.%s' % pylib), 'tifffile')]
 if 0:#sys.platform.startswith('linux'):
     datas += [(os.path.join(pylibpath, 'libglut.*'), 'lib')]
 
 if not PLUGIN:
     #datas += [(os.path.join(site, 'javabridge', '*.%s' % pylib), 'javabridge'), (os.path.join(site, 'javabridge', 'jars', '*'), os.path.join('javabridge', 'jars')), (os.path.join(site, 'bioformats', 'jars', '*'), os.path.join('bioformats', 'jars'))]
-    datas += [(os.path.join(site, 'javabridge', 'jars', '*'), os.path.join('javabridge', 'jars')), (os.path.join(site, 'bioformats', 'jars', '*'), os.path.join('bioformats', 'jars'))]#, (os.path.join(os.path.dirname(site), 'lib-dynload', '_posixsubprocess.cpython-37m-x86_64-linux-gnu.so'), os.path.join('lib', 'python3.7', 'lib-dynload'))]
+    try:
+        import javabridge,  bioformats
+        jv = os.path.dirname(javabridge.__file__)
+        bf = os.path.dirname(os.path.dirname(bioformats.__file__))
+        datas += [(os.path.join(jv, 'jars', '*'), os.path.join('javabridge', 'jars')), (os.path.join(bf, 'bioformats', 'jars', '*'), os.path.join('bioformats', 'jars'))]
+    except ImportError:
+        pass
+    try:
+        import nd2
+        nd2 = os.path.dirname(nd2.__file__)
+        datas += [(os.path.join(nd2, '*.typed'), 'nd2')]
+    except ImportError:
+        pass
+
+    #if 1:#sys.platform.startswith('win'): # v=0.7.1
+    #    datas += [(os.path.join(nd2, '*.typed'), 'nd2')]
+    #else:
+    #    datas += [(os.path.join(nd2, '_sdk', '*'), os.path.join('nd2', '_sdk'))]
+    #datas += [(os.path.join(site, 'javabridge', 'jars', '*'), os.path.join('javabridge', 'jars')), (os.path.join(site, 'bioformats', 'jars', '*'), os.path.join('bioformats', 'jars'))]
 
 a = Analysis([prog],
              pathex=[code],

Chromagnon/PriCommon/flatConv.py

@@ -12,7 +12,7 @@
 try:
     import wx
     import time
-    from common import guiFuncs as G
+    from . import guiFuncs as G
     _wx = True
 except ImportError:
     _wx = False
@@ -263,7 +263,7 @@ def view(self, target):
             """
             view with viewer
             """
-            import ndviewer
+            from PriCommon import ndviewer
             import sys
             # prepare viewer
             if not self.aui:
@@ -290,8 +290,8 @@ def view(self, target):
 
     usage = r"""%prog imgFiles [options]"""
     p = optparse.OptionParser(usage=usage)
-    p.add_option('--suffix', '-S', default=SUF,
-                 help='suffix for the output file names (default inputfile + %s)' % SUF)
+    p.add_option('--out', '-O',
+                 help='output file name (default inputfile + %s)' % EXT)
     p.add_option('--flatFile', '-F',
                  help='flatFielding file required for flatfielding')
     p.add_option('--make', '-m', action='store_true',
@@ -306,21 +306,25 @@ def view(self, target):
     else:
         make = options.make
         del options.make
+        #fns = arguments#[0]
+        #args = arguments[1:]
 
         fns = []
         for fn in arguments:
             fns += glob.glob(os.path.expandvars(os.path.expanduser(fn)))
 
         if make:
-            outs = [makeFlatConv(fn, suffix=EXT) for fn in fns]
+            outs = [makeFlatConv(fn) for fn in fns]
             if len(outs) > 1:
-                out = os.path.commonprefix(outs) + EXT
-                out = imgio.merge(outs, out, along='w')
+                if options.out:
+                    out = options.out
+                else:
+                    out = os.path.commonprefix(outs) + EXT
+                out = O.copyImgs.merge(outs, out, mergeAlong='w')
                 [os.remove(out) for out in outs]
             else:
                 out = outs[0]
             print(out, ' saved')
         else:
             for fn in fns:
-                out = flatConv(fn, **options.__dict__)
-                print(out, ' done')
+                print(flatConv(fn, **options.__dict__), ' done')

Chromagnon/PriCommon/imgFilters.py

@@ -1,10 +1,9 @@
 #!/usr/bin/env python
 from __future__ import print_function
-
 try:
-    from Priithon.all import N, U, Y, F
+    from ..Priithon.all import N, U, Y, F, Mrc
 except (ValueError, ImportError):
-    from ..Priithon.all import N, U, Y, F
+    from Priithon.all import N, U, Y, F, Mrc
 from scipy import optimize
 try:
     from . import imgFit
@@ -955,7 +954,7 @@ def findMaxWithGFitAll(img, thre=0, sigma_peak=0.5, npts=100, win=11, mask_npxls
         else:
             v = ret[1]
             zyx = ret[2:2+ndim]
-            if N.any(N.abs(zyx - vzyx[-ndim:]) > win/2.):#zyx < 0 or zyx > img.shape or ):
+            if N.any(N.abs(zyx - vzyx[1:]) > win/2.):#zyx < 0 or zyx > img.shape or ):
                 mask_value(img, vzyx[-ndim:], r=mask_npxls, value=img.min())
                 poses.append(list(vzyx)[0:1] + [vzyx[-ndim:]] + [sigma_peak])
             else:

Chromagnon/PriCommon/imgFit.py

@@ -1,9 +1,9 @@
 ### Here all kinds of fitting
 from __future__ import print_function
 try:
-    from Priithon.all import N, U
-except (ValueError, ImportError):
     from ..Priithon.all import N, U
+except (ValueError, ImportError):
+    from Priithon.all import N, U
 try:
     from . import imgFilters, imgGeo
 except ValueError:

Chromagnon/PriCommon/imgGeo.py

@@ -85,7 +85,7 @@ def affine(a, r, mag, tyx=(0,0), center=(0,0)):
 
 def affine_index(indexarray, r, mag, tyx=(0,0), center=None):
     if center is None:
-        center = N.array(indexarray.shape[-2:], N.float) / 2.
+        center = N.array(indexarray.shape[-2:], float) / 2.
 
     rotRadian = N.pi / 180. * r
     cosTheta = N.cos(rotRadian)

Chromagnon/PriCommon/imgResample.py

@@ -1,10 +1,9 @@
 try:
-    from Priithon.all import U, N
-    from common import ppro26 as ppro
-except (ValueError, ImportError):
     from ..Priithon.all import U, N
-    from ..common import ppro26 as ppro
+except (ValueError, ImportError):
+    from Priithon.all import U, N
 
+from . import ppro26 as ppro
 NCPU = ppro.NCPU
 
 import scipy.ndimage.interpolation as ndii
@@ -113,7 +112,7 @@ def trans3D_affine(arr, tzyx=(0,0,0), r=0, mag=1, dzyx=(0,0,0), rzy=0, ncpu=NCPU
 
         arr = canvas
 
-    if dtype in (N.int, N.uint8, N.uint16, N.uint32):
+    if dtype in (int, N.uint8, N.uint16, N.uint32):
         arr = N.where(arr < 0, 0, arr)
 
     return arr.astype(dtype)
@@ -146,8 +145,8 @@ def getOffset(shape, invmat, ty, tx, start=0):
 
 def affine_transform(arr, invmat, offset=0.0, order=ORDER):
     return U.nd.affine_transform(arr, invmat, offset,
-                               output=N.float32, cval=arr.min(), order=order)
-                               #output=N.float32, cval=0, order=order)
+                               #output=N.float32, cval=arr.min(), order=order)
+                               output=N.float32, cval=0, order=order)
 
 
 # 

Chromagnon/PriCommon/xcorr.py

@@ -256,8 +256,6 @@ def Xcorr(a, b, phaseContrast=PHASE, nyquist=NYQUIST, gFit=True, win=11, ret=Non
         afa = af
         bfa = bf
         fact = N.std(a) * N.std(b) * a.size
-        if not fact:
-            fact = 1
     del a, b, af, bf
 
     targetShape = shape #+ (npad * 2)

Chromagnon/Priithon/plt/plot_objects.py

@@ -75,12 +75,13 @@ def draw_point_list(start,stop,pen,dc):
         start and stop are 2xN arrays of x,y point coordinates.  N lines
         are drawn, one between each of the start,stop pairs using the
         specified pen.  The lines are drawn on the given device context, dc.    
-    """    
+    """
+    #print('draw_point_list')
     dc.SetPen(pen)
     for i in range(len(start)):
         pt1 = start[i]
         pt2 = stop[i]
-        dc.DrawLine(pt1[0],pt1[1],pt2[0],pt2[1])
+        dc.DrawLine(int(pt1[0]),int(pt1[1]),int(pt2[0]),int(pt2[1]))
     dc.SetPen(wx.NullPen)
 
 #-----------------------------------------------------------------------#
@@ -752,6 +753,7 @@ def draw_fast(self,dc):
         color = get_color(self.color)
         pen = wx.Pen(color, self.weight, style)        
         dc.SetPen(pen)
+        #print('draw_fast')
         dc.DrawLines(self.single_line)
         dc.SetPen(wx.NullPen)
 
@@ -785,8 +787,10 @@ def draw(self, dc):
             style = line_style_map[self.style]
             dc.SetPen(wx.Pen(color, self.weight,style))
             try:
+                #print('draw')
                 dc.DrawLines(self.scaled)           
             except:
+                #print('draw except')
                 dc.DrawLines(list(map(tuple,self.scaled)))
             dc.SetPen(wx.NullPen)
 
@@ -848,12 +852,12 @@ def _down_triangle(self, dc, xc, yc, size=1):
                         (0.0,0.577350*size*6)],xc,yc)
 
     def _cross(self, dc, xc, yc, size=1):
-        dc.DrawLine(xc-3*size,yc-3*size,xc+3*size,yc+3*size)
-        dc.DrawLine(xc-3*size,yc+3*size,xc+3*size,yc-3*size)
+        dc.DrawLine(int(xc-3*size),int(yc-3*size),int(xc+3*size),int(yc+3*size))
+        dc.DrawLine(int(xc-3*size),int(yc+3*size),int(xc+3*size),int(yc-3*size))
 
     def _plus(self, dc, xc, yc, size=1):
-        dc.DrawLine(xc-3*size,yc,xc+3*size,yc)
-        dc.DrawLine(xc,yc-3*size,xc,yc+3*size)
+        dc.DrawLine(int(xc-3*size),int(yc),int(xc+3*size),int(yc))
+        dc.DrawLine(int(xc),int(yc-3*size),int(xc),int(yc+3*size))
 
 class line_object(poly_points):
     """ Combines poly_line and poly_marker into a single
@@ -964,8 +968,8 @@ def bounding_box(self):
         return bb
 
     def scale_and_shift(self, scale=1, shift=0,upperleft=None,size=None):
-        if scale is 1: scale = array((1,1))
-        if shift is 0: shift = array((0,0))
+        if scale == 1: scale = array((1,1))
+        if shift == 0: shift = array((0,0))
         graph_pixels_per_axis_unit = scale
         self.scale = graph_pixels_per_axis_unit/self.image_pixels_per_axis_unit
         self.origin = shift

Chromagnon/Priithon/splitND2.py

@@ -137,7 +137,7 @@ def __init__(self, data, colorAxis=-3, title='', size=None,
         if not isinstance(data, F.mockNDarray):
             data = N.asanyarray(data) # 20060720 - numpy arrays don't have ndim attribute
         # 20180308
-        if data.dtype.type in [N.bool, N.uint32, N.uint64]:
+        if data.dtype.type in [bool, N.uint32, N.uint64]:
             data = data.astype(N.uint16)
         elif data.dtype.type in [N.int32, N.int64, ]:
             data = data.astype(N.int16)

Chromagnon/Priithon/viewerCommon.py

@@ -546,9 +546,13 @@ def OnMouse(self, ev):
 
         self.SetCurrent(self.context)        
         #x,y = ev.m_x,  self.m_h-ev.m_y
-        x, y = ev.GetPosition() # 20141127
-        y = self.m_h - y
-        xEff_float, yEff_float= gluUnProject(x,y,0)[:2]
+       # x, y = ev.GetPosition() # 20141127
+       # y = self.m_h - y
+        #xEff_float, yEff_float= gluUnProject(x,y,0)[:2] # does not work on M2 Mac 20230225
+        x = ev.GetX()
+        y = self.m_h-ev.GetY()
+        x0, y0, scale, aspR = self.m_x0, self.m_y0, self.m_scale, self.m_aspectRatio
+        xEff_float, yEff_float = int( (x-x0)/scale ) , int( (y-y0)/(scale*aspR) ) 
 
         # 20080701:  in new coord system, integer pixel coord go through the center of pixel