def to_multicanvas(self,
canvas,
sequential=False,
sans=False,
modnames=True):
""" """
c_in = []
c_out = []
creduced, cnull = self.descriptors[0].in_and_out_canvas(canvas)
c_in.append(creduced)
c_out.append(cnull)
for desc in self.descriptors[1:]:
if sequential:
creduced, cnull = desc.in_and_out_canvas(cnull)
else:
creduced, cnull = desc.in_and_out_canvas(canvas)
c_in.append(creduced)
c_out.append(cnull)
outnames = self.aliases
if not sans:
c_final = c_in
else:
c_final = c_out
if modnames:
outnames = ['sans %s' % name for name in outnames]
mcout = MultiCanvas(canvii=c_final, names=outnames)
mcout.set_colors(*self.colors, fillnull=True)
return mcout
def to_multicanvas(self, canvas, sequential=False, sans=False,
modnames=True):
""" """
c_in = [] ; c_out = []
creduced, cnull = self.descriptors[0].in_and_out_canvas(canvas)
c_in.append(creduced) ; c_out.append(cnull)
for desc in self.descriptors[1:] :
if sequential:
creduced, cnull = desc.in_and_out_canvas(cnull)
else:
creduced, cnull = desc.in_and_out_canvas(canvas)
c_in.append(creduced) ; c_out.append(cnull)
outnames = self.aliases
if not sans:
c_final = c_in
else:
c_final = c_out
if modnames:
outnames = ['sans %s' % name for name in outnames]
mcout = MultiCanvas(canvii=c_final, names=outnames)
mcout.set_colors(*self.colors, fillnull=True)
return mcout
def run_main(self):
""" Define a series of sub-functions so logging/traceback easier """
def getPARAM(attr, null=None):
""" Geattr on self.PARAMS with optional null to return empty lists
or dicts instead of None """
return getattr(self.PARAMS, attr, null)
def mkfromrootdir(dirname):
""" Make a directory relative to self.ARGS.root; log it """
fullpath = op.join(self.ARGS.outroot, dirname)
self.logmkdir(fullpath)
return fullpath
@continue_on_fail
def MPLOT(mcattr, mcpltfcn, mcpltkwds, outdirectory):
""" boilerplate reduction; if multiplot parameter, runs the plot."""
if getPARAM(mcattr):
mcpltfcn, mcpltkwds = getattr(mc, mcpltfcn), getPARAM(mcpltkwds, null={})
mcpltfcn(**mcpltkwds)
self.logsavefig(op.join(outdirectory, getPARAM(mcattr) ))
summary = open(op.join(self.ARGS.outroot, SUMMARYFILE), 'a') #make method
stream = self.PARAMS.parameter_stream()
paramspath = op.join(self.ARGS.outroot, PARAMSFILE)
self.logstream(paramspath, '\n\n'.join(stream))
# MULTICANVAS OPERATIONS
#-----------------------
self.LOGGER.info("Creating MultiCanvas...")
if self.PARAMS.mapper is None:
self.PARAMS.mapper = []
mc = MultiCanvas.from_labeled(self.ARGS.image,
storecolors=self.PARAMS.storecolors,
ignore=self.PARAMS.ignore,
mapper = self.PARAMS.mapper
)
def sumwrite(string, newlines='\n\n', indent=''):
summary.write(indent + string + newlines)
sumwrite(mc.__repr__())
multidir = mkfromrootdir(self.PARAMS.multidir)
MPLOT('multihist', 'hist', 'multihistkwds', multidir)
MPLOT('multipie', 'pie', 'multipiekwds', multidir)
MPLOT('multishow', 'show', 'multishowkwds', multidir)
# CANVAS OPERATIONS
#-----------------------
#Early exit if not canvas operations
if not getattr(self.PARAMS, 'canvasdir', None):
return
@continue_on_fail
def canvas_stats(canvas, name='STATS'):
""" Writes a text stream of various canvas parameters. """
head = '### %s ###'% name
sumwrite(head, newlines='\n')
sumwrite('-' * len(head))
sumwrite(canvas.__repr__())
sumwrite("Image Resolution: %s"% str(canvas.rez), indent=_INDENT)
sumwrite("Particle coverage: %.2f%%" %
round(100*canvas.pixarea, _ROUND), indent=_INDENT)
for attr in getPARAM('summary_attr'):
val = getattr(canvas, attr)
xmin, xmax, xmean = min(val), max(val), np.mean(val)
sumwrite("%s (min, max, mean): (%.2f - %.2f, %.2f)"
% (attr, xmin, xmax, xmean), indent=_INDENT)
sumwrite('')
@continue_on_fail
def canvas_hist(canvas, attr, savepath=None, **histkwds):
""" Histogram of canvas attribute """
attr_array = getattr(canvas, attr)
plt.hist(attr_array, **histkwds)
plt.xlabel(attr)
plt.ylabel('counts')
if savepath:
self.logsavefig(savepath)
self.LOGGER.info("Creating Canvas List")
# List of new canvas and canvas-by-canvas breakdown
total_canvas = mc.to_canvas(mapcolors=True)
#X Don't mess w/ order, net canvas must be first (see below idx==0)
ALLITEMS = [(getPARAM('canvasdir', null='Net Canvas'), total_canvas)]
if getPARAM('canvas_by_canvas'):
ALLITEMS.extend(mc.items())
canbycandir = mkfromrootdir('canvas_by_canvas')
# Stats of each canvas pairwise
for idx, (name, canvas) in enumerate(ALLITEMS):
if idx == 0:
workingcanvasdir = mkfromrootdir(name)
else:
workingcanvasdir = mkfromrootdir('%s/%s' % (canbycandir, name))
autocolor = None
if getPARAM('autocolor'):
if idx != 0:
autocolor = mc._request_plotcolors()[idx-1]
# Set canvas background
if getPARAM('canvas_background'):
canvas = canvas.set_bg(getPARAM('canvas_background'))
canvas_stats(canvas, name)
# Color/ Gray/ Binary image #Maybe refactor in future boilerplate
if getPARAM('colorimage'):
colorkwds = getPARAM('showkwds', null={})
canvas.show(**colorkwds)
self.logsavefig(op.join(workingcanvasdir, '%s_colored.png' % name))
if getPARAM('grayimage'):
graykwds = getPARAM('graykwds', null={})
if 'cmap' not in graykwds:
graykwds['cmap'] = 'gray'
canvas.show(**graykwds)
self.logsavefig(op.join(workingcanvasdir, '%s_gray.png' % name))
if getPARAM('binaryimage'):
binarykwds = getPARAM('binarykwds', null={})
binarykwds.update({'cmap':'pbinary'})
canvas.show(**binarykwds)
self.logsavefig(op.join(workingcanvasdir, '%s_binary.png' % name))
# Scatter plots
for (x,y) in getPARAM('scatter', null=[]):
scatterkwds = getPARAM('scatterkwds')
if autocolor and 'color' not in scatterkwds: #Don't use update
canvas.scatter(attr1=x, attr2=y, color=autocolor, **scatterkwds)
else:
canvas.scatter(attr1=x, attr2=y, **scatterkwds)
self.logsavefig(op.join(workingcanvasdir, '%s_scatter.png' % name))
# Generate histograms
for attr in getPARAM('summary_attr'):
savepath = op.join(workingcanvasdir, '%s_hist.png'%name)
histkwds = getPARAM('histkwds', null={})
if autocolor and 'color' not in histkwds:
canvas_hist(canvas, attr, color=autocolor,
savepath=savepath, **histkwds)
else:
canvas_hist(canvas, attr, savepath=savepath, **histkwds)
summary.close()
def run_main(self):
""" Define a series of sub-functions so logging/traceback easier """
def getPARAM(attr, null=None):
""" Geattr on self.PARAMS with optional null to return empty lists
or dicts instead of None """
return getattr(self.PARAMS, attr, null)
def mkfromrootdir(dirname):
""" Make a directory relative to self.ARGS.root; log it """
fullpath = op.join(self.ARGS.outroot, dirname)
self.logmkdir(fullpath)
return fullpath
@continue_on_fail
def MPLOT(mcattr, mcpltfcn, mcpltkwds, outdirectory):
""" boilerplate reduction; if multiplot parameter, runs the plot."""
if getPARAM(mcattr):
mcpltfcn, mcpltkwds = getattr(mc,
mcpltfcn), getPARAM(mcpltkwds,
null={})
mcpltfcn(**mcpltkwds)
self.logsavefig(op.join(outdirectory, getPARAM(mcattr)))
summary = open(op.join(self.ARGS.outroot, SUMMARYFILE),
'a') #make method
stream = self.PARAMS.parameter_stream()
paramspath = op.join(self.ARGS.outroot, PARAMSFILE)
self.logstream(paramspath, '\n\n'.join(stream))
# MULTICANVAS OPERATIONS
#-----------------------
self.LOGGER.info("Creating MultiCanvas...")
if self.PARAMS.mapper is None:
self.PARAMS.mapper = []
mc = MultiCanvas.from_labeled(self.ARGS.image,
storecolors=self.PARAMS.storecolors,
ignore=self.PARAMS.ignore,
mapper=self.PARAMS.mapper)
def sumwrite(string, newlines='\n\n', indent=''):
summary.write(indent + string + newlines)
sumwrite(mc.__repr__())
multidir = mkfromrootdir(self.PARAMS.multidir)
MPLOT('multihist', 'hist', 'multihistkwds', multidir)
MPLOT('multipie', 'pie', 'multipiekwds', multidir)
MPLOT('multishow', 'show', 'multishowkwds', multidir)
# CANVAS OPERATIONS
#-----------------------
#Early exit if not canvas operations
if not getattr(self.PARAMS, 'canvasdir', None):
return
@continue_on_fail
def canvas_stats(canvas, name='STATS'):
""" Writes a text stream of various canvas parameters. """
head = '### %s ###' % name
sumwrite(head, newlines='\n')
sumwrite('-' * len(head))
sumwrite(canvas.__repr__())
sumwrite("Image Resolution: %s" % str(canvas.rez), indent=_INDENT)
sumwrite("Particle coverage: %.2f%%" %
round(100 * canvas.pixarea, _ROUND),
indent=_INDENT)
for attr in getPARAM('summary_attr'):
val = getattr(canvas, attr)
xmin, xmax, xmean = min(val), max(val), np.mean(val)
sumwrite("%s (min, max, mean): (%.2f - %.2f, %.2f)" %
(attr, xmin, xmax, xmean),
indent=_INDENT)
sumwrite('')
@continue_on_fail
def canvas_hist(canvas, attr, savepath=None, **histkwds):
""" Histogram of canvas attribute """
attr_array = getattr(canvas, attr)
plt.hist(attr_array, **histkwds)
plt.xlabel(attr)
plt.ylabel('counts')
if savepath:
self.logsavefig(savepath)
self.LOGGER.info("Creating Canvas List")
# List of new canvas and canvas-by-canvas breakdown
total_canvas = mc.to_canvas(mapcolors=True)
#X Don't mess w/ order, net canvas must be first (see below idx==0)
ALLITEMS = [(getPARAM('canvasdir', null='Net Canvas'), total_canvas)]
if getPARAM('canvas_by_canvas'):
ALLITEMS.extend(mc.items())
canbycandir = mkfromrootdir('canvas_by_canvas')
# Stats of each canvas pairwise
for idx, (name, canvas) in enumerate(ALLITEMS):
if idx == 0:
workingcanvasdir = mkfromrootdir(name)
else:
workingcanvasdir = mkfromrootdir('%s/%s' % (canbycandir, name))
autocolor = None
if getPARAM('autocolor'):
if idx != 0:
autocolor = mc._request_plotcolors()[idx - 1]
# Set canvas background
if getPARAM('canvas_background'):
canvas = canvas.set_bg(getPARAM('canvas_background'))
canvas_stats(canvas, name)
# Color/ Gray/ Binary image #Maybe refactor in future boilerplate
if getPARAM('colorimage'):
colorkwds = getPARAM('showkwds', null={})
canvas.show(**colorkwds)
self.logsavefig(
op.join(workingcanvasdir, '%s_colored.png' % name))
if getPARAM('grayimage'):
graykwds = getPARAM('graykwds', null={})
if 'cmap' not in graykwds:
graykwds['cmap'] = 'gray'
canvas.show(**graykwds)
self.logsavefig(op.join(workingcanvasdir,
'%s_gray.png' % name))
if getPARAM('binaryimage'):
binarykwds = getPARAM('binarykwds', null={})
binarykwds.update({'cmap': 'pbinary'})
canvas.show(**binarykwds)
self.logsavefig(
op.join(workingcanvasdir, '%s_binary.png' % name))
# Scatter plots
for (x, y) in getPARAM('scatter', null=[]):
scatterkwds = getPARAM('scatterkwds')
if autocolor and 'color' not in scatterkwds: #Don't use update
canvas.scatter(attr1=x,
attr2=y,
color=autocolor,
**scatterkwds)
else:
canvas.scatter(attr1=x, attr2=y, **scatterkwds)
self.logsavefig(
op.join(workingcanvasdir, '%s_scatter.png' % name))
# Generate histograms
for attr in getPARAM('summary_attr'):
savepath = op.join(workingcanvasdir, '%s_hist.png' % name)
histkwds = getPARAM('histkwds', null={})
if autocolor and 'color' not in histkwds:
canvas_hist(canvas,
attr,
color=autocolor,
savepath=savepath,
**histkwds)
else:
canvas_hist(canvas, attr, savepath=savepath, **histkwds)
summary.close()
