def reloadAll(prefix=None, debug=False):
"""Automatically reload everything whose __file__ begins with prefix.
- Skips reload if the file has not been updated (if .pyc is newer than .py)
- if prefix is None, checks all loaded modules
"""
for modName, mod in sys.modules.items(): ## don't use iteritems; size may change during reload
if not inspect.ismodule(mod):
continue
if modName == '__main__':
continue
## Ignore if the file name does not start with prefix
if not hasattr(mod, '__file__') or os.path.splitext(mod.__file__)[1] not in ['.py', '.pyc']:
continue
if prefix is not None and mod.__file__[:len(prefix)] != prefix:
continue
## ignore if the .pyc is newer than the .py (or if there is no pyc or py)
py = os.path.splitext(mod.__file__)[0] + '.py'
pyc = py + 'c'
if os.path.isfile(pyc) and os.path.isfile(py) and os.stat(pyc).st_mtime >= os.stat(py).st_mtime:
#if debug:
#print "Ignoring module %s; unchanged" % str(mod)
continue
try:
reload(mod, debug=debug)
except:
printExc("Error while reloading module %s, skipping\n" % mod)
def makeARGB(data, lut=None, levels=None, useRGBA=False):
"""
Convert a 2D or 3D array into an ARGB array suitable for building QImages
Will optionally do scaling and/or table lookups to determine final colors.
Returns the ARGB array (values 0-255) and a boolean indicating whether there is alpha channel data.
Arguments:
data - 2D or 3D numpy array of int/float types
For 2D arrays (x, y):
* The color will be determined using a lookup table (see argument 'lut').
* If levels are given, the data is rescaled and converted to int
before using the lookup table.
For 3D arrays (x, y, rgba):
* The third axis must have length 3 or 4 and will be interpreted as RGBA.
* The 'lut' argument is not allowed.
lut - Lookup table for 2D data. May be 1D or 2D (N,rgba) and must have dtype=ubyte.
Values in data will be converted to color by indexing directly from lut.
Lookup tables can be built using GradientWidget.
levels - List [min, max]; optionally rescale data before converting through the
lookup table. rescaled = (data-min) * len(lut) / (max-min)
useRGBA - If True, the data is returned in RGBA order. The default is
False, which returns in BGRA order for use with QImage.
"""
prof = debug.Profiler('functions.makeARGB', disabled=True)
## sanity checks
if data.ndim == 3:
if data.shape[2] not in (3, 4):
raise Exception("data.shape[2] must be 3 or 4")
#if lut is not None:
#raise Exception("can not use lookup table with 3D data")
elif data.ndim != 2:
raise Exception("data must be 2D or 3D")
if lut is not None:
if lut.ndim == 2:
if lut.shape[1] not in (3, 4):
raise Exception("lut.shape[1] must be 3 or 4")
elif lut.ndim != 1:
raise Exception("lut must be 1D or 2D")
if lut.dtype != np.ubyte:
raise Exception(
'lookup table must have dtype=ubyte (got %s instead)' %
str(lut.dtype))
if levels is not None:
levels = np.array(levels)
if levels.shape == (2, ):
pass
elif levels.shape in [(3, 2), (4, 2)]:
if data.ndim == 3:
raise Exception("Can not use 2D levels with 3D data.")
if lut is not None:
raise Exception(
'Can not use 2D levels and lookup table together.')
else:
raise Exception("Levels must have shape (2,) or (3,2) or (4,2)")
prof.mark('1')
if lut is not None:
lutLength = lut.shape[0]
else:
lutLength = 256
## weave requires contiguous arrays
global USE_WEAVE
if (levels is not None or lut is not None) and USE_WEAVE:
data = np.ascontiguousarray(data)
## Apply levels if given
if levels is not None:
try: ## use weave to speed up scaling
if not USE_WEAVE:
raise Exception(
'Weave is disabled; falling back to slower version.')
if levels.ndim == 1:
scale = float(lutLength) / (levels[1] - levels[0])
offset = float(levels[0])
data = rescaleData(data, scale, offset)
else:
if data.ndim == 2:
newData = np.empty(data.shape + (levels.shape[0], ),
dtype=np.uint32)
for i in xrange(levels.shape[0]):
scale = float(lutLength /
(levels[i, 1] - levels[i, 0]))
offset = float(levels[i, 0])
newData[..., i] = rescaleData(data, scale, offset)
elif data.ndim == 3:
newData = np.empty(data.shape, dtype=np.uint32)
for i in xrange(data.shape[2]):
scale = float(lutLength /
(levels[i, 1] - levels[i, 0]))
offset = float(levels[i, 0])
#print scale, offset, data.shape, newData.shape, levels.shape
newData[..., i] = rescaleData(data[..., i], scale,
offset)
data = newData
except:
if USE_WEAVE:
debug.printExc("Error; disabling weave.")
USE_WEAVE = False
if levels.ndim == 1:
if data.ndim == 2:
levels = levels[np.newaxis, np.newaxis, :]
else:
levels = levels[np.newaxis, np.newaxis, np.newaxis, :]
else:
levels = levels[np.newaxis, np.newaxis, ...]
if data.ndim == 2:
data = data[..., np.newaxis]
data = ((data - levels[..., 0]) * lutLength) / (levels[..., 1] -
levels[..., 0])
prof.mark('2')
## apply LUT if given
if lut is not None and data.ndim == 2:
if data.dtype.kind not in ('i', 'u'):
data = data.astype(int)
data = np.clip(data, 0, lutLength - 1)
try:
if not USE_WEAVE:
raise Exception(
'Weave is disabled; falling back to slower version.')
newData = np.empty((data.size, ) + lut.shape[1:], dtype=np.uint8)
flat = data.reshape(data.size)
size = data.size
ncol = lut.shape[1]
newStride = newData.strides[0]
newColStride = newData.strides[1]
lutStride = lut.strides[0]
lutColStride = lut.strides[1]
flatStride = flat.strides[0] / flat.dtype.itemsize
#print "newData:", newData.shape, newData.dtype
#print "flat:", flat.shape, flat.dtype, flat.min(), flat.max()
#print "lut:", lut.shape, lut.dtype
#print "size:", size, "ncols:", ncol
#print "strides:", newStride, newColStride, lutStride, lutColStride, flatStride
code = """
for( int i=0; i<size; i++ ) {
for( int j=0; j<ncol; j++ ) {
newData[i*newStride + j*newColStride] = lut[flat[i*flatStride]*lutStride + j*lutColStride];
}
}
"""
scipy.weave.inline(code, [
'flat', 'lut', 'newData', 'size', 'ncol', 'newStride',
'lutStride', 'flatStride', 'newColStride', 'lutColStride'
])
data = newData.reshape(data.shape + lut.shape[1:])
except:
if USE_WEAVE:
debug.printExc("Error; disabling weave.")
USE_WEAVE = False
data = lut[data]
else:
if data.dtype is not np.ubyte:
data = np.clip(data, 0, 255).astype(np.ubyte)
prof.mark('3')
## copy data into ARGB ordered array
imgData = np.empty(data.shape[:2] + (4, ), dtype=np.ubyte)
if data.ndim == 2:
data = data[..., np.newaxis]
prof.mark('4')
if useRGBA:
order = [0, 1, 2, 3] ## array comes out RGBA
else:
order = [
2, 1, 0, 3
] ## for some reason, the colors line up as BGR in the final image.
if data.shape[2] == 1:
for i in xrange(3):
imgData[..., order[i]] = data[..., 0]
else:
for i in xrange(0, data.shape[2]):
imgData[..., order[i]] = data[..., i]
prof.mark('5')
if data.shape[2] == 4:
alpha = True
else:
alpha = False
imgData[..., 3] = 255
prof.mark('6')
prof.finish()
return imgData, alpha
def makeARGB(data, lut=None, levels=None, useRGBA=False):
"""
Convert a 2D or 3D array into an ARGB array suitable for building QImages
Will optionally do scaling and/or table lookups to determine final colors.
Returns the ARGB array (values 0-255) and a boolean indicating whether there is alpha channel data.
Arguments:
data - 2D or 3D numpy array of int/float types
For 2D arrays (x, y):
* The color will be determined using a lookup table (see argument 'lut').
* If levels are given, the data is rescaled and converted to int
before using the lookup table.
For 3D arrays (x, y, rgba):
* The third axis must have length 3 or 4 and will be interpreted as RGBA.
* The 'lut' argument is not allowed.
lut - Lookup table for 2D data. May be 1D or 2D (N,rgba) and must have dtype=ubyte.
Values in data will be converted to color by indexing directly from lut.
Lookup tables can be built using GradientWidget.
levels - List [min, max]; optionally rescale data before converting through the
lookup table. rescaled = (data-min) * len(lut) / (max-min)
useRGBA - If True, the data is returned in RGBA order. The default is
False, which returns in BGRA order for use with QImage.
"""
prof = debug.Profiler('functions.makeARGB', disabled=True)
## sanity checks
if data.ndim == 3:
if data.shape[2] not in (3,4):
raise Exception("data.shape[2] must be 3 or 4")
#if lut is not None:
#raise Exception("can not use lookup table with 3D data")
elif data.ndim != 2:
raise Exception("data must be 2D or 3D")
if lut is not None:
if lut.ndim == 2:
if lut.shape[1] not in (3,4):
raise Exception("lut.shape[1] must be 3 or 4")
elif lut.ndim != 1:
raise Exception("lut must be 1D or 2D")
if lut.dtype != np.ubyte:
raise Exception('lookup table must have dtype=ubyte (got %s instead)' % str(lut.dtype))
if levels is not None:
levels = np.array(levels)
if levels.shape == (2,):
pass
elif levels.shape in [(3,2), (4,2)]:
if data.ndim == 3:
raise Exception("Can not use 2D levels with 3D data.")
if lut is not None:
raise Exception('Can not use 2D levels and lookup table together.')
else:
raise Exception("Levels must have shape (2,) or (3,2) or (4,2)")
prof.mark('1')
if lut is not None:
lutLength = lut.shape[0]
else:
lutLength = 256
## weave requires contiguous arrays
global USE_WEAVE
if (levels is not None or lut is not None) and USE_WEAVE:
data = np.ascontiguousarray(data)
## Apply levels if given
if levels is not None:
try: ## use weave to speed up scaling
if not USE_WEAVE:
raise Exception('Weave is disabled; falling back to slower version.')
if levels.ndim == 1:
scale = float(lutLength) / (levels[1]-levels[0])
offset = float(levels[0])
data = rescaleData(data, scale, offset)
else:
if data.ndim == 2:
newData = np.empty(data.shape+(levels.shape[0],), dtype=np.uint32)
for i in xrange(levels.shape[0]):
scale = float(lutLength / (levels[i,1]-levels[i,0]))
offset = float(levels[i,0])
newData[...,i] = rescaleData(data, scale, offset)
elif data.ndim == 3:
newData = np.empty(data.shape, dtype=np.uint32)
for i in xrange(data.shape[2]):
scale = float(lutLength / (levels[i,1]-levels[i,0]))
offset = float(levels[i,0])
#print scale, offset, data.shape, newData.shape, levels.shape
newData[...,i] = rescaleData(data[...,i], scale, offset)
data = newData
except:
if USE_WEAVE:
debug.printExc("Error; disabling weave.")
USE_WEAVE = False
if levels.ndim == 1:
if data.ndim == 2:
levels = levels[np.newaxis, np.newaxis, :]
else:
levels = levels[np.newaxis, np.newaxis, np.newaxis, :]
else:
levels = levels[np.newaxis, np.newaxis, ...]
if data.ndim == 2:
data = data[..., np.newaxis]
data = ((data-levels[...,0]) * lutLength) / (levels[...,1]-levels[...,0])
prof.mark('2')
## apply LUT if given
if lut is not None and data.ndim == 2:
if data.dtype.kind not in ('i', 'u'):
data = data.astype(int)
data = np.clip(data, 0, lutLength-1)
try:
if not USE_WEAVE:
raise Exception('Weave is disabled; falling back to slower version.')
newData = np.empty((data.size,) + lut.shape[1:], dtype=np.uint8)
flat = data.reshape(data.size)
size = data.size
ncol = lut.shape[1]
newStride = newData.strides[0]
newColStride = newData.strides[1]
lutStride = lut.strides[0]
lutColStride = lut.strides[1]
flatStride = flat.strides[0] / flat.dtype.itemsize
#print "newData:", newData.shape, newData.dtype
#print "flat:", flat.shape, flat.dtype, flat.min(), flat.max()
#print "lut:", lut.shape, lut.dtype
#print "size:", size, "ncols:", ncol
#print "strides:", newStride, newColStride, lutStride, lutColStride, flatStride
code = """
for( int i=0; i<size; i++ ) {
for( int j=0; j<ncol; j++ ) {
newData[i*newStride + j*newColStride] = lut[flat[i*flatStride]*lutStride + j*lutColStride];
}
}
"""
scipy.weave.inline(code, ['flat', 'lut', 'newData', 'size', 'ncol', 'newStride', 'lutStride', 'flatStride', 'newColStride', 'lutColStride'])
data = newData.reshape(data.shape + lut.shape[1:])
except:
if USE_WEAVE:
debug.printExc("Error; disabling weave.")
USE_WEAVE = False
data = lut[data]
else:
if data.dtype is not np.ubyte:
data = np.clip(data, 0, 255).astype(np.ubyte)
prof.mark('3')
## copy data into ARGB ordered array
imgData = np.empty(data.shape[:2]+(4,), dtype=np.ubyte)
if data.ndim == 2:
data = data[..., np.newaxis]
prof.mark('4')
if useRGBA:
order = [0,1,2,3] ## array comes out RGBA
else:
order = [2,1,0,3] ## for some reason, the colors line up as BGR in the final image.
if data.shape[2] == 1:
for i in xrange(3):
imgData[..., order[i]] = data[..., 0]
else:
for i in xrange(0, data.shape[2]):
imgData[..., order[i]] = data[..., i]
prof.mark('5')
if data.shape[2] == 4:
alpha = True
else:
alpha = False
imgData[..., 3] = 255
prof.mark('6')
prof.finish()
return imgData, alpha