def make_pressure_color_arrays(vesselgraph):
edges = vesselgraph.edgelist
flags = vesselgraph.edges['flags']
data = vesselgraph.nodes['pressure']
num_nodes = len(vesselgraph.nodes['position'])
nflags = krebsutils.edge_to_node_property(num_nodes, edges, flags, 'or')
is_set = lambda flags_, flag: np.asarray(np.bitwise_and(flags_, flag), np.
bool)
gray = np.asarray((0.1, 0.1, 0.1))
lgray = np.asarray((0.5, 0.5, 0.5))
circulated = is_set(flags, krebsutils.CIRCULATED)
ncirculated = is_set(nflags, krebsutils.CIRCULATED)
capillary = is_set(flags, krebsutils.CAPILLARY)
ncapillary = is_set(nflags, krebsutils.CAPILLARY)
p0 = np.amin(data[ncirculated])
p1 = np.amax(data[ncirculated])
cm = matplotlib.cm.ScalarMappable(cmap=cm_redblue)
cm.set_clim(p0, p1)
edgedata = np.average((data[edges[:, 0]], data[edges[:, 1]]), axis=0)
edgecolors = cm.to_rgba(edgedata)[:, :3]
edgecolors[~circulated] = gray
#edgecolors[capillary] = lgray
nodecolors = cm.to_rgba(data)[:, :3]
nodecolors[~ncirculated] = gray
#nodecolors[ncapillary] = lgray
vesselgraph.edges['colors'] = edgecolors
vesselgraph.nodes['colors'] = nodecolors
def plots(self,x):
figax= train_data.plot(color='b',alpha=0.1,s=10)
train_data.plot(lambda x: self.catastrophe, color='r',alpha=1,s=20,figax=figax)
plt.savefig('../results/outliers.png')
for i in xrange(6):
crap = numpy.sort(self.dm.data_dm().x[:,i])
crap= crap[len(crap)*.1:len(crap)*.9]
sig = crap.std()
cm=matplotlib.cm.ScalarMappable(
norm=matplotlib.colors.Normalize(vmin=crap[len(crap)/2]-5*sig,
vmax=crap[len(crap)/2]+5*sig),cmap='Spectral')
cval=cm.to_rgba(self.dm.data_dm().x[:,i])
figax= train_data.plot(c=cval,alpha=0.3,s=20,cmap=cm)
figax[0].suptitle(str(i))
plt.savefig('../results/splits.'+str(i)+'.png')
figax= self.dm.data_dm().plot(color='r',alpha=0.1,s=10,ndim=6)
self.dm.data_dm().plot(lambda x: self.catastrophe,
color='b',alpha=0.1,s=20,ndim=6,figax=figax)
plt.savefig('../results/temp.png')
figax= self.dm.data_dm().plot(color='r',alpha=0.1,s=10,nsig=20,ndim=6)
self.dm.data_dm().plot(lambda x: self.catastrophe,
color='b',alpha=0.2,s=20,ndim=6,figax=figax)
plt.savefig('../results/temp2.png')
cm=matplotlib.cm.ScalarMappable(cmap='rainbow')
cval=cm.to_rgba(self.weight(x.x))
figax= x.plot(c=cval,alpha=0.2,s=20,cmap=cm,vmin=0,vmax=cval.max())
plt.savefig('../results/color_dm.png')
def write_kml(filename, data, col, cmap):
ns = 'http://www.opengis.net/kml/2.2'
ns_prefix = '{' + ns + '}'
kml = ET.Element(ns_prefix + 'kml')
document = ET.SubElement(kml, ns_prefix + 'Document')
document_name = ET.SubElement(document, ns_prefix + 'name')
document_name.text = OUT_HEADER[col]
document_name.tail = '\n'
norm = matplotlib.colors.Normalize(vmin=data[:,col].min(), vmax=data[:,col].max())
cm = matplotlib.cm.ScalarMappable(norm=norm, cmap=cmap)
for i in range(data.shape[0] - 1):
color = cm.to_rgba(data[i,col], bytes=True)
color_string = f'{color[0]:02x}{color[1]:02x}{color[2]:02x}'
placemark = ET.SubElement(document, ns_prefix + 'Placemark')
placemark.tail = '\n'
placemark_name = ET.SubElement(placemark, ns_prefix + 'name')
placemark_name.text = f'{OUT_HEADER[col]} = {data[i,col]}'
description = ET.SubElement(placemark, ns_prefix + 'description')
description.text = f'time = {timestamp_to_string(data[i,OUT_COL_TIME])}'
linestring = ET.SubElement(placemark, ns_prefix + 'LineString')
coordinates = ET.SubElement(linestring, ns_prefix + 'coordinates')
coordinates.text = '%f,%f %f,%f' % (data[i,OUT_COL_LON], data[i,OUT_COL_LAT], data[i+1,OUT_COL_LON], data[i+1,OUT_COL_LAT])
style = ET.SubElement(placemark, ns_prefix + 'Style')
linestyle = ET.SubElement(style, ns_prefix + 'LineStyle')
linecolor = ET.SubElement(linestyle, ns_prefix + 'color')
linecolor.text = color_string
width = ET.SubElement(linestyle, ns_prefix + 'width')
width.text = '4'
tree = ET.ElementTree(kml)
with open(filename, 'wb') as outf:
tree.write(outf, encoding='utf-8', xml_declaration=True, default_namespace=ns)
def matplotlibColormapToPovray(name, cm):
import matplotlib.cm
N = 256
lims = cm.get_clim()
colors = cm.to_rgba(np.linspace(lims[0], lims[1], N))
colors = colors[:, :3] # skip alpha channel
colors = np.power(colors, 2.4)
return Colormap(name, lims, colors)
def get_attimg(image, attmap, cm=matplotlib.cm.ScalarMappable(cmap="jet")):
h, w = image.size(1), image.size(2)
s = attmap.size(-1)
attmap = attmap.squeeze().view(s, s).data.cpu().numpy()
attmap = resize(attmap, (h, w), mode='reflect')
attmap = cm.to_rgba(attmap)[:, :, 0:3]
attmap = torch.from_numpy(attmap).float().permute(2, 0, 1)
return image + attmap
def run(self, workspace):
header = ("Image", "Objects", "Bin # (innermost=1)", "Bin count", "Fraction", "Intensity", "COV")
stats = []
d = {}
for image in self.images:
for o in self.objects:
for bin_count_settings in self.bin_counts:
stats += \
self.do_measurements(workspace,
image.image_name.value,
o.object_name.value,
o.center_object_name.value
if o.center_choice != C_SELF
else None,
o.center_choice.value,
bin_count_settings,
d)
if self.wants_zernikes:
self.calculate_zernikes(workspace)
if self.show_window:
workspace.display_data.header = header
workspace.display_data.stats = stats
workspace.display_data.heatmaps = []
for heatmap in self.heatmaps:
heatmap_img = d.get(id(heatmap))
if heatmap_img is not None:
if self.show_window or heatmap.wants_to_save_display:
labels = workspace.object_set.get_objects(
heatmap.object_name.get_objects_name()).segmented
if self.show_window:
workspace.display_data.heatmaps.append(
(heatmap_img, labels != 0))
if heatmap.wants_to_save_display:
colormap = heatmap.colormap.value
if colormap == matplotlib.cm.gray.name:
output_pixels = heatmap_img
else:
if colormap == cps.DEFAULT:
colormap = cpprefs.get_default_colormap()
cm = matplotlib.cm.ScalarMappable(
cmap=colormap)
output_pixels = cm.to_rgba(heatmap_img)[:, :, :3]
output_pixels[labels == 0, :] = 0
parent_image = workspace.image_set.get_image(
heatmap.image_name.get_image_name())
output_img = cpi.Image(
output_pixels,
parent_image=parent_image)
img_name = heatmap.display_name.value
workspace.image_set.add(img_name, output_img)
def run(self, workspace):
header = ("Image", "Objects", "Bin # (innermost=1)", "Bin count", "Fraction", "Intensity", "COV")
stats = []
d = {}
for image in self.images:
for o in self.objects:
for bin_count_settings in self.bin_counts:
stats += \
self.do_measurements(workspace,
image.image_name.value,
o.object_name.value,
o.center_object_name.value
if o.center_choice != C_SELF
else None,
o.center_choice.value,
bin_count_settings,
d)
if self.wants_zernikes != Z_NONE:
self.calculate_zernikes(workspace)
if self.show_window:
workspace.display_data.header = header
workspace.display_data.stats = stats
workspace.display_data.heatmaps = []
for heatmap in self.heatmaps:
heatmap_img = d.get(id(heatmap))
if heatmap_img is not None:
if self.show_window or heatmap.wants_to_save_display:
labels = workspace.object_set.get_objects(
heatmap.object_name.get_objects_name()).segmented
if self.show_window:
workspace.display_data.heatmaps.append(
(heatmap_img, labels != 0))
if heatmap.wants_to_save_display:
colormap = heatmap.colormap.value
if colormap == matplotlib.cm.gray.name:
output_pixels = heatmap_img
else:
if colormap == cps.DEFAULT:
colormap = cpprefs.get_default_colormap()
cm = matplotlib.cm.ScalarMappable(
cmap=colormap)
output_pixels = cm.to_rgba(heatmap_img)[:, :, :3]
output_pixels[labels == 0, :] = 0
parent_image = workspace.image_set.get_image(
heatmap.image_name.get_image_name())
output_img = cpi.Image(
output_pixels,
parent_image=parent_image)
img_name = heatmap.display_name.value
workspace.image_set.add(img_name, output_img)
def _compute_colors(cls, x):
import matplotlib.cm
# Get RGB color map proportional to the concentration.
cm = matplotlib.cm.ScalarMappable()
crgba = cm.to_rgba(x, bytes=True)
# Convert RGB to HEX
colors = []
for row in crgba:
# get R,G,B of RGBA
colors.append(_rgb_to_hex(tuple(list(row[0:3]))))
# Convert Hex to Decimal
for i, c in enumerate(colors):
colors[i] = int(c, 0)
return colors
def get(self):
logging.info('GET self.request.body = {}'.format(self.request.body))
reqType = self.request.get('reqType')
if reqType == 'getJobInfo':
job = SpatialJobWrapper.get_by_id(int(self.request.get('id')))
if self.user.user_id() != job.user_id:
self.response.headers['Content-Type'] = 'application/json'
self.response.write({
"status": False,
"msg": "Not the right user"
})
result = {}
stdout = ''
stderr = ''
complete = ''
if job.outData is None:
complete = 'yes'
else:
try:
fstdoutHandle = open(str(job.outData + '/stdout.log'), 'r')
stdout = fstdoutHandle.read()
fstdoutHandle.close()
fstderrHandle = open(str(job.outData + '/stderr.log'), 'r')
stderr = fstderrHandle.read()
fstderrHandle.close()
if os.path.exists("{0}/results/complete".format(
job.outData)):
complete = 'yes'
except IOError as e:
traceback.print_exc()
result['status'] = False
result[
'msg'] = 'Error running the simulation: stdout/stderr outputs missing.'
result.update({
"id": int(self.request.get('id')),
"jobStatus": job.status,
"complete": complete,
"resource": job.resource,
"modelName": job.modelName,
"outData": job.outData,
"name": job.name,
"uuid": job.cloudDatabaseID,
"output_stored": job.output_stored,
"stdout": stdout,
"stderr": stderr,
"indata": json.loads(job.indata)
})
logging.debug("result =\n\n{}".format(pprint.pformat(result)))
self.response.headers['Content-Type'] = 'application/json'
self.response.write(json.dumps(result))
return
elif reqType == 'getMeshData':
try:
job = SpatialJobWrapper.get_by_id(int(self.request.get('id')))
data = json.loads(self.request.get('data'))
logging.debug("data = {}".format(data))
trajectory = data["trajectory"]
timeIdx = data["timeIdx"]
resultJS = {}
#if not job.preprocessed or not os.path.exists(job.preprocessedDir):
job.preprocess(trajectory)
indir = job.preprocessedDir
with open(os.path.join(indir, 'mesh.json'), 'r') as meshfile:
mesh = json.load(meshfile)
with open(os.path.join(indir, 'voxelTuples.json'),
'r') as voxelTuplesFile:
voxelTuples = json.load(voxelTuplesFile)
f = os.path.join(indir, 'result{0}'.format(trajectory))
with h5py.File(f, 'r') as dataFile:
species = dataFile.keys()
self.response.content_type = 'application/json'
self.response.write(
json.dumps({
"mesh": mesh,
"voxelTuples": voxelTuples,
"species": species
}))
except Exception as e:
traceback.print_exc()
result = {}
result['status'] = False
result['msg'] = 'Error: error fetching results {0}'.format(e)
self.response.headers['Content-Type'] = 'application/json'
self.response.write(json.dumps(result))
return
elif reqType == 'getTimeSeriesData':
try:
job = SpatialJobWrapper.get_by_id(int(self.request.get('id')))
data = json.loads(self.request.get('data'))
logging.debug(
'patial.get(onlyColorRange): data={0}'.format(data))
trajectory = data["trajectory"]
sTime = data["timeStart"]
eTime = data["timeEnd"]
#TODO: what is the right value here?
if eTime is None:
eTime = 0
dataType = "population" if "showPopulation" in data and data[
"showPopulation"] else "concentration"
resultJS = {}
if job.preprocessed is None or trajectory not in job.preprocessed or not os.path.exists(
job.preprocessedDir):
job.preprocess(trajectory)
f = os.path.join(job.preprocessedDir,
'result{0}'.format(trajectory))
limits = {}
logging.debug(
'Spatial.get(onlyColorRange): sTime={0} eTime={0}'.format(
sTime, eTime))
with h5py.File(f, 'r') as dataFile:
dataTmp = {}
colorTmp = {}
for specie in dataFile.keys():
data2 = dataFile[specie][dataType][sTime:eTime + 1]
dataTmp[specie] = data2
limits[specie] = {
'min': dataFile[specie][dataType].attrs['min'],
'max': dataFile[specie][dataType].attrs['max']
}
cm.set_clim(dataFile[specie][dataType].attrs['min'],
dataFile[specie][dataType].attrs['max'])
rgbas = cm.to_rgba(data2, bytes=True).astype('uint32')
rgbas = numpy.left_shift(
rgbas[:, :, 0], 16) + numpy.left_shift(
rgbas[:, :, 1], 8) + rgbas[:, :, 2]
#rgbaInts = numpy.zeros((rgbas.shape[0], rgbas.shape[1]))
#for i in range(rgbas.shape[0]):
# for j in range(rgbas.shape[1]):
# rgbaInts[i, j] = int('0x%02x%02x%02x' % tuple(rgbas[i, j][0:3]), 0)
colorTmp[specie] = []
for i in range(rgbas.shape[0]):
colorTmp[specie].append(
list(rgbas[i].astype('int')))
colors = {}
data = {}
for i in range(abs(eTime - sTime + 1)):
colors[sTime + i] = {}
data[sTime + i] = {}
for specie in dataFile.keys():
colors[sTime + i][specie] = colorTmp[specie][i]
data[sTime + i][specie] = list(dataTmp[specie][i])
self.response.content_type = 'application/json'
self.response.write(
json.dumps({
"colors": colors,
"raw": data,
"limits": limits
}))
except Exception as e:
traceback.print_exc()
result = {}
result['status'] = False
result['msg'] = 'Error: error fetching results {0}'.format(e)
self.response.headers['Content-Type'] = 'application/json'
self.response.write(json.dumps(result))
return
self.render_response('spatial.html')
def make_any_color_arrays(vesselgraph, data_name):
edges = vesselgraph.edgelist
num_nodes = len(vesselgraph.nodes['position'])
flags = vesselgraph.edges['flags']
flags = np.asarray(flags, dtype='uint32')
nflags = krebsutils.edge_to_node_property(num_nodes, edges, flags, 'or')
mask = myutils.bbitwise_and(flags, krebsutils.CIRCULATED)
nmask = myutils.bbitwise_and(nflags, krebsutils.CIRCULATED)
if data_name in vesselgraph.edges:
edgedata = vesselgraph.edges[data_name]
nodedata = krebsutils.edge_to_node_property(num_nodes, edges, edgedata,
'avg')
else:
nodedata = vesselgraph.nodes[data_name]
edgedata = np.average((nodedata[edges[:, 0]], nodedata[edges[:, 1]]),
axis=0)
gray = np.asarray((0.1, 0.1, 0.1))
edgecolors = np.repeat(gray.reshape(1, -1), len(edgedata), axis=0)
nodecolors = np.repeat(gray.reshape(1, -1), len(nodedata), axis=0)
#colors = lambda arr: cm.to_rgba(arr)[:,:3]
colors = lambda arr: np.power(cm.to_rgba(arr)[:, :3], 2.4)
if data_name == 'hematocrit':
cm = matplotlib.cm.ScalarMappable(cmap=cm_hematocrit)
cm.set_clim(0, 1)
unmapped_range = (0., 1.)
edgecolors[mask] = colors(edgedata[mask])
nodecolors[nmask] = colors(nodedata[nmask])
elif data_name == 'pressure':
#this looks really ugly if there is a zero pressure node
#p0 = np.amin(nodedata)
p0 = np.min(nodedata[np.nonzero(nodedata)])
p1 = np.amax(nodedata)
unmapped_range = (p0, p1)
cm = matplotlib.cm.ScalarMappable(cmap=cm_redblue)
cm.set_clim(p0, p1)
edgecolors[mask] = colors(edgedata[mask])
nodecolors[nmask] = colors(nodedata[nmask])
elif data_name == 'shearforce':
mask = mask & (edgedata > 0)
nmask = nmask & (nodedata > 0)
edgedata = edgedata[mask]
nodedata = nodedata[nmask]
unmapped_range = edgedata.min(), edgedata.max()
edgedata = np.log10(edgedata)
nodedata = np.log10(nodedata)
p0 = -4 #np.amin(edgedata)
p1 = -1 #np.amax(edgedata)
cm = matplotlib.cm.ScalarMappable(cmap=matplotlib.cm.spectral)
cm.set_clim(p0, p1)
edgecolors[mask] = colors(edgedata)
nodecolors[nmask] = colors(nodedata)
elif data_name == 'S_tot':
#mask = mask & (edgedata>0)
#nmask = nmask & (nodedata>0)
edgedata = edgedata[mask]
nodedata = nodedata[nmask]
unmapped_range = edgedata.min(), edgedata.max()
p0 = np.amin(edgedata)
p1 = np.amax(edgedata)
#print("p0: %f, p1: %f" % (p0,p1))
#unmapped_range = (p0, p1)
cm = matplotlib.cm.ScalarMappable(cmap=matplotlib.cm.jet)
cm.set_clim(p0, p1)
#edgedata = np.log10(edgedata)
#nodedata = np.log10(nodedata)
#p0 = -4#np.amin(edgedata)
#p1 = -1#np.amax(edgedata)
#cm = matplotlib.cm.ScalarMappable(cmap=matplotlib.cm.spectral)
#cm.set_clim(p0, p1)
edgecolors[mask] = colors(edgedata)
nodecolors[nmask] = colors(nodedata)
elif data_name == 'flow':
mask = mask & (edgedata > 0)
nmask = nmask & (nodedata > 0)
edgedata = edgedata[mask]
nodedata = nodedata[nmask]
unmapped_range = edgedata.min(), edgedata.max()
edgedata = np.log10(edgedata)
nodedata = np.log10(nodedata)
p0 = np.floor(np.amin(edgedata))
p1 = np.ceil(np.amax(edgedata))
cm = matplotlib.cm.ScalarMappable(cmap=matplotlib.cm.jet)
cm.set_clim(p0, p1)
edgecolors[mask] = colors(edgedata)
nodecolors[nmask] = colors(nodedata)
elif data_name == 'conductivitySignal':
edgedata = edgedata[mask]
nodedata = nodedata[nmask]
unmapped_range = edgedata.min(), edgedata.max()
p0 = np.amin(edgedata)
p1 = np.amax(edgedata)
cm = matplotlib.cm.ScalarMappable(cmap=matplotlib.cm.jet)
cm.set_clim(p0, p1)
edgecolors[mask] = colors(edgedata)
nodecolors[nmask] = colors(nodedata)
elif data_name == 'metabolicSignal':
edgedata = edgedata[mask]
nodedata = nodedata[nmask]
unmapped_range = edgedata.min(), edgedata.max()
p0 = np.amin(edgedata)
p1 = np.amax(edgedata)
cm = matplotlib.cm.ScalarMappable(cmap=matplotlib.cm.jet)
cm.set_clim(p0, p1)
edgecolors[mask] = colors(edgedata)
nodecolors[nmask] = colors(nodedata)
elif data_name == 'flags':
edgecolors[mask
& (flags & krebsutils.ARTERY).astype(np.bool)] = np.asarray(
(1., 0., 0.))
nodecolors[nmask & (nflags
& krebsutils.ARTERY).astype(np.bool)] = np.asarray(
(1., 0., 0.))
edgecolors[mask
& (flags & krebsutils.VEIN).astype(np.bool)] = np.asarray(
(0., 0., 1.))
nodecolors[nmask
& (nflags & krebsutils.VEIN).astype(np.bool)] = np.asarray(
(0., 0., 1.))
edgecolors[mask
& (flags
& krebsutils.CAPILLARY).astype(np.bool)] = np.asarray(
(0., 1., 0.))
nodecolors[nmask
& (nflags
& krebsutils.CAPILLARY).astype(np.bool)] = np.asarray(
(0., 1., 0.))
for idx in vesselgraph.roots:
nodecolors[idx] = np.asarray((1., 1., 0.))
cm, unmapped_range = None, (None, None)
vesselgraph.edges['colors'] = edgecolors
vesselgraph.nodes['colors'] = nodecolors
return cm, unmapped_range
def get(self):
logging.info('GET self.request.body = {}'.format(self.request.body))
reqType = self.request.get('reqType')
if reqType == 'getJobInfo':
job = SpatialJobWrapper.get_by_id(int(self.request.get('id')))
if self.user.user_id() != job.user_id:
self.response.headers['Content-Type'] = 'application/json'
self.response.write({ "status" : False, "msg" : "Not the right user" })
result = {}
stdout = ''
stderr = ''
complete = ''
if job.outData is None:
complete = 'yes'
else:
try:
fstdoutHandle = open(str(job.outData + '/stdout.log'), 'r')
stdout = fstdoutHandle.read()
fstdoutHandle.close()
fstderrHandle = open(str(job.outData + '/stderr.log'), 'r')
stderr = fstderrHandle.read()
fstderrHandle.close()
if os.path.exists("{0}/results/complete".format(job.outData)):
complete = 'yes'
except IOError as e:
traceback.print_exc()
result['status'] = False
result['msg'] = 'Error running the simulation: stdout/stderr outputs missing.'
result.update({"id" : int(self.request.get('id')),
"jobStatus" : job.status,
"complete" : complete,
"resource" : job.resource,
"modelName" : job.modelName,
"outData" : job.outData,
"name" : job.name,
"uuid": job.cloudDatabaseID,
"output_stored": job.output_stored,
"stdout" : stdout,
"stderr" : stderr,
"indata" : json.loads(job.indata) })
logging.debug("result =\n\n{}".format(pprint.pformat(result)))
self.response.headers['Content-Type'] = 'application/json'
self.response.write(json.dumps(result))
return
elif reqType == 'getMeshData':
try:
job = SpatialJobWrapper.get_by_id(int(self.request.get('id')))
data = json.loads(self.request.get('data'))
logging.debug("data = {}".format(data))
trajectory = data["trajectory"]
timeIdx = data["timeIdx"]
resultJS = {}
#if not job.preprocessed or not os.path.exists(job.preprocessedDir):
job.preprocess(trajectory)
indir = job.preprocessedDir
with open(os.path.join(indir, 'mesh.json') ,'r') as meshfile:
mesh = json.load(meshfile)
with open(os.path.join(indir, 'voxelTuples.json') ,'r') as voxelTuplesFile:
voxelTuples = json.load(voxelTuplesFile)
f = os.path.join(indir, 'result{0}'.format(trajectory))
with h5py.File(f, 'r') as dataFile:
species = dataFile.keys()
self.response.content_type = 'application/json'
self.response.write(json.dumps({ "mesh" : mesh, "voxelTuples" : voxelTuples, "species" : species }))
except Exception as e:
traceback.print_exc()
result = {}
result['status'] = False
result['msg'] = 'Error: error fetching results {0}'.format(e)
self.response.headers['Content-Type'] = 'application/json'
self.response.write(json.dumps(result))
return
elif reqType == 'getTimeSeriesData':
try:
job = SpatialJobWrapper.get_by_id(int(self.request.get('id')))
data = json.loads(self.request.get('data'))
logging.debug('patial.get(onlyColorRange): data={0}'.format(data))
trajectory = data["trajectory"]
sTime= data["timeStart"]
eTime = data["timeEnd"]
#TODO: what is the right value here?
if eTime is None:
eTime = 0
dataType = "population" if "showPopulation" in data and data["showPopulation"] else "concentration"
resultJS = {}
if job.preprocessed is None or trajectory not in job.preprocessed or not os.path.exists(job.preprocessedDir):
job.preprocess(trajectory)
f = os.path.join(job.preprocessedDir, 'result{0}'.format(trajectory))
limits = {}
logging.debug('Spatial.get(onlyColorRange): sTime={0} eTime={0}'.format(sTime,eTime))
with h5py.File(f, 'r') as dataFile:
dataTmp = {}
colorTmp = {}
for specie in dataFile.keys():
data2 = dataFile[specie][dataType][sTime:eTime + 1]
dataTmp[specie] = data2
limits[specie] = { 'min' : dataFile[specie][dataType].attrs['min'],
'max' : dataFile[specie][dataType].attrs['max'] }
cm.set_clim(dataFile[specie][dataType].attrs['min'], dataFile[specie][dataType].attrs['max'])
rgbas = cm.to_rgba(data2, bytes = True).astype('uint32')
rgbas = numpy.left_shift(rgbas[:, :, 0], 16) + numpy.left_shift(rgbas[:, :, 1], 8) + rgbas[:, :, 2]
#rgbaInts = numpy.zeros((rgbas.shape[0], rgbas.shape[1]))
#for i in range(rgbas.shape[0]):
# for j in range(rgbas.shape[1]):
# rgbaInts[i, j] = int('0x%02x%02x%02x' % tuple(rgbas[i, j][0:3]), 0)
colorTmp[specie] = []
for i in range(rgbas.shape[0]):
colorTmp[specie].append(list(rgbas[i].astype('int')))
colors = {}
data = {}
for i in range(abs(eTime - sTime + 1)):
colors[sTime + i] = {}
data[sTime + i] = {}
for specie in dataFile.keys():
colors[sTime + i][specie] = colorTmp[specie][i]
data[sTime + i][specie] = list(dataTmp[specie][i])
self.response.content_type = 'application/json'
self.response.write(json.dumps( { "colors" : colors, "raw" : data, "limits" : limits } ))
except Exception as e:
traceback.print_exc()
result = {}
result['status'] = False
result['msg'] = 'Error: error fetching results {0}'.format(e)
self.response.headers['Content-Type'] = 'application/json'
self.response.write(json.dumps(result))
return
self.render_response('spatial.html')
def InsertGraphColors(vesselgraph, po2field, data_name):
edges = vesselgraph.edgelist
num_nodes = len(vesselgraph.nodes['position'])
if data_name in vesselgraph.edges:
edgedata = data = vesselgraph.edges[data_name]
nodedata = krebsutils.edge_to_node_property(num_nodes, edges, data,
'avg')
else:
nodedata = data = vesselgraph.nodes[data_name]
edgedata = np.average((data[edges[:, 0]], data[edges[:, 1]]), axis=0)
if data_name == 'po2vessels':
try:
p1 = np.amax(data)
except ValueError:
print("p1 not found")
pass
if po2field is not None:
p1 = max(p1, np.amax(po2field))
try:
p0 = np.amin(data)
except ValueError:
print("p0 not found")
pass
if po2field is not None:
p0 = min(p0, np.amin(po2field))
#p1 = math.ceil(p1/10.0)*10.0 # round to powers of something
#p1 = 100.0
value_range = (p0, p1)
cm = matplotlib.cm.ScalarMappable(cmap=cm_po2)
elif data_name == 'saturation':
cm = matplotlib.cm.ScalarMappable(cmap=matplotlib.cm.spectral)
vesselgraph.edges['saturation']
value_range = (np.min(vesselgraph.edges['saturation']),
np.max(vesselgraph.edges['saturation']))
#value_range = (0,1.)
elif data_name == 'hboconc':
cm = matplotlib.cm.ScalarMappable(cmap=matplotlib.cm.gnuplot)
p1 = math.ceil(np.amax(data))
value_range = (0., p1)
cm.set_clim(*value_range)
colors = lambda arr: np.power(cm.to_rgba(arr)[:, :3], 2.4)
if data_name in vesselgraph.edges:
edgecolors = colors(data)
nodecolors = colors(nodedata)
else:
edgecolors = colors(edgedata)
nodecolors = colors(data)
flags = vesselgraph.edges['flags']
nflags = krebsutils.edge_to_node_property(num_nodes, edges, flags, 'or')
is_not_set = lambda flags_, flag: np.bitwise_not(
np.asarray(np.bitwise_and(flags_, flag), np.bool))
gray = np.asarray((0.3, 0.3, 0.3))
uncirculated = is_not_set(flags, krebsutils.CIRCULATED)
nuncirculated = is_not_set(nflags, krebsutils.CIRCULATED)
edgecolors[uncirculated] = gray
nodecolors[nuncirculated] = gray
print 'colormap range ', cm.get_clim()
vesselgraph.edges['colors'] = edgecolors
vesselgraph.nodes['colors'] = nodecolors
return cm
# Compile images
cm = matplotlib.cm.ScalarMappable(None, cmap='plasma')
cm.set_clim(0.00, 0.08)
disparities = np.load(os.path.join(cfg['disp_path'], cfg['disp_fmt'].format(cfg['filenames_index'])), mmap_mode='r')
full_image = np.zeros((2 * len(cfg['sets']) * cfg['image_size'][0], len(cfg['distances']) * cfg['image_size'][1], 3), dtype=np.uint8)
for si, s in enumerate(cfg['sets']):
print('Set: {}'.format(s))
imgs = np.zeros((cfg['image_size'][0], len(cfg['distances']) * cfg['image_size'][1], 3), dtype=np.uint8)
disps = np.zeros_like(imgs)
for di, d in enumerate(cfg['distances']):
fn = cfg['filename_fmt'].format(set=s, scene=cfg['scene'], object=cfg['object'], distance=d)
mask_fn = cfg['mask_fmt'].format(set=s, scene=cfg['scene'], object=cfg['object'], distance=d)
img = imread(os.path.join(cfg['data_path'], fn))
img = img_as_ubyte(resize(img, cfg['image_size']))
imgs[:, (di * cfg['image_size'][1]):((di + 1) * cfg['image_size'][1])] = img
mask = imread(os.path.join(cfg['data_path'], mask_fn))[:, :, 0]
mask = resize(mask, cfg['image_size'])
c = find_contours(mask, 0.5)[0]
disp = disparities[indices[(s, d)], :, :]
disp = resize(disp, cfg['image_size'])
disp = img_as_ubyte(cm.to_rgba(disp)[:, :, :3])
rr, cc = polygon_perimeter(c[:, 0], c[:, 1])
outline = np.zeros(cfg['image_size'])
outline[rr, cc] = 1
outline = binary_dilation(outline, square(5))
disp[outline, :] = [255, 255, 255]
disps[:, (di * cfg['image_size'][1]):((di + 1) * cfg['image_size'][1])] = disp
full_image[((si * 2) * cfg['image_size'][0]):((si * 2 + 1) * cfg['image_size'][0]), :] = imgs
full_image[((si * 2 + 1) * cfg['image_size'][0]):((si * 2 + 2) * cfg['image_size'][0]), :] = disps
imsave(cfg['output_path'], full_image)
def make_any_color_arrays(vesselgraph, data_name):
edges = vesselgraph.edgelist
num_nodes = len(vesselgraph.nodes['position'])
flags = vesselgraph.edges['flags']
nflags = krebsutils.edge_to_node_property(num_nodes, edges, flags, 'or')
mask = myutils.bbitwise_and(flags, krebsutils.CIRCULATED)
nmask = myutils.bbitwise_and(nflags, krebsutils.CIRCULATED)
if data_name in vesselgraph.edges:
edgedata = vesselgraph.edges[data_name]
nodedata = krebsutils.edge_to_node_property(num_nodes, edges, edgedata,
'avg')
else:
nodedata = vesselgraph.nodes[data_name]
edgedata = np.average((nodedata[edges[:, 0]], nodedata[edges[:, 1]]),
axis=0)
gray = np.asarray((0.1, 0.1, 0.1))
edgecolors = np.repeat(gray.reshape(1, -1), len(edgedata), axis=0)
nodecolors = np.repeat(gray.reshape(1, -1), len(nodedata), axis=0)
#colors = lambda arr: cm.to_rgba(arr)[:,:3]
colors = lambda arr: np.power(cm.to_rgba(arr)[:, :3], 2.4)
if data_name == 'hematocrit':
cm = matplotlib.cm.ScalarMappable(cmap=cm_hematocrit)
cm.set_clim(0, 1)
unmapped_range = (0., 1.)
edgecolors[mask] = colors(edgedata[mask])
nodecolors[nmask] = colors(nodedata[nmask])
elif data_name == 'pressure':
p0 = np.amin(nodedata)
p1 = np.amax(nodedata)
unmapped_range = (p0, p1)
cm = matplotlib.cm.ScalarMappable(cmap=cm_redblue)
cm.set_clim(p0, p1)
edgecolors[mask] = colors(edgedata[mask])
nodecolors[nmask] = colors(nodedata[nmask])
elif data_name == 'shearforce':
mask = mask & (edgedata > 0)
nmask = nmask & (nodedata > 0)
edgedata = edgedata[mask]
nodedata = nodedata[nmask]
unmapped_range = edgedata.min(), edgedata.max()
edgedata = np.log10(edgedata)
nodedata = np.log10(nodedata)
p0 = -4 #np.amin(edgedata)
p1 = -1 #np.amax(edgedata)
cm = matplotlib.cm.ScalarMappable(cmap=matplotlib.cm.spectral)
cm.set_clim(p0, p1)
edgecolors[mask] = colors(edgedata)
nodecolors[nmask] = colors(nodedata)
elif data_name == 'flow':
mask = mask & (edgedata > 0)
nmask = nmask & (nodedata > 0)
edgedata = edgedata[mask]
nodedata = nodedata[nmask]
unmapped_range = edgedata.min(), edgedata.max()
edgedata = np.log10(edgedata)
nodedata = np.log10(nodedata)
p0 = np.floor(np.amin(edgedata))
p1 = np.ceil(np.amax(edgedata))
cm = matplotlib.cm.ScalarMappable(cmap=matplotlib.cm.jet)
cm.set_clim(p0, p1)
edgecolors[mask] = colors(edgedata)
nodecolors[nmask] = colors(nodedata)
elif data_name == 'flags':
unmapped_range = (0., 1.)
mask = mask & (edgedata > 0)
nmask = nmask & (nodedata > 0)
edgedata = edgedata[mask]
nodedata = nodedata[nmask]
edgedata = np.bitwise_and(edgedata, krebsutils.ARTERY)
cm = matplotlib.cm.ScalarMappable(cmap=matplotlib.cm.jet)
edgecolors[mask] = colors(edgedata)
nodecolors[nmask] = colors(nodedata)
vesselgraph.edges['colors'] = edgecolors
vesselgraph.nodes['colors'] = nodecolors
return cm, unmapped_range