class PyFaceProgress(IProgress):
def initialize(self, title, max_index):
self.progress = ProgressDialog(title="Characterizing %d peaks on current image"%max_index,
max=int(max_index), show_time=True, can_cancel=False)
self.progress.open()
def increment(self):
self.current_idx+=1
self.progress.update(self.current_idx)
def open_project(self, path):
with open(path, 'rb') as fp:
if fp.read(15) != 'Spacetime\nJSON\n':
raise ValueError('not a valid Spacetime project file')
data = json.load(fp)
progress = ProgressDialog(title="Open", message="Loading project", max=len(data)+1, can_cancel=False, parent=self.context.uiparent)
progress.open()
with self.context.canvas.hold_delayed():
self.tabs[0].from_serialized(data.pop(0)[1])
tabs = [self.tabs[0]]
progress.update(1)
# FIXME: check version number and emit warning
for p, (id, props) in enumerate(data):
try:
tab = self.get_new_tab(self.moduleloader.get_class_by_id(id))
tab.from_serialized(props)
tabs.append(tab)
except KeyError:
support.Message.show(title='Warning', message='Warning: incompatible project file', desc='Ignoring unknown graph id "{0}". Project might not be completely functional.'.format(id))
progress.update(2+p)
self.tabs = tabs
self.project_path = path
wx.CallAfter(self.clear_project_modified)
wx.CallAfter(lambda: (progress.update(progress.max), progress.close()))
def locate_peaks(self):
peaks=[]
progress = ProgressDialog(title="Peak finder progress", message="Finding peaks on %s images"%self.numfiles, max=self.numfiles, show_time=True, can_cancel=False)
progress.open()
for idx in xrange(self.numfiles):
self.controller.set_active_index(idx)
self.data = self.controller.get_active_image()[:]
self.CC = cv_funcs.xcorr(self.template, self.data)
# peak finder needs peaks greater than 1. Multiply by 255 to scale them.
pks=pc.two_dim_findpeaks(self.CC*255, peak_width=self.peak_width, medfilt_radius=None)
pks[:,2]=pks[:,2]/255.
peaks.append(pks)
progress.update(idx+1)
#ipdb.set_trace()
self.peaks=peaks
self.redraw_plots()
def _get_misc_data(self):
if not self.raw:
return
if self.show_gui:
# progress dialog with indefinite progress bar
prog = ProgressDialog(title="Loading SQD data...",
message="Loading stim channel data from SQD "
"file ...")
prog.open()
prog.update(0)
else:
prog = None
try:
data, times = self.raw[self.misc_chs]
except Exception as err:
if self.show_gui:
error(None, "Error reading SQD data file: %s (Check the "
"terminal output for details)" % str(err),
"Error Reading SQD File")
raise
finally:
if self.show_gui:
prog.close()
return data
def do_reload(self, info): app = info.ui.context['object'] progress = ProgressDialog(title="Reload", message="Reloading data", max=len(app.tabs)+1, can_cancel=True, parent=app.context.uiparent) progress.open() with app.drawmgr.hold(): for i, tab in enumerate(app.tabs): tab.reload = True cont, skip = progress.update(i+1) if not cont or skip: break progress.update(progress.max) progress.close()
def _create_fsaverage_fired(self):
# progress dialog with indefinite progress bar
title = "Creating FsAverage ..."
message = "Copying fsaverage files ..."
prog = ProgressDialog(title=title, message=message)
prog.open()
prog.update(0)
try:
self.model.create_fsaverage()
except Exception as err:
error(None, str(err), "Error Creating FsAverage")
raise
finally:
prog.close()
def locate_peaks(self):
from hyperspy import peak_char as pc
peaks=[]
"""from hyperspy.misc.progressbar import ProgressBar, \
Percentage, RotatingMarker, ETA, Bar
widgets = ['Locating peaks: ', Percentage(), ' ', Bar(marker=RotatingMarker()),
' ', ETA()]
pbar = ProgressBar(widgets=widgets, maxval=100).start()"""
progress = ProgressDialog(title="Peak finder progress", message="Finding peaks on %s images"%self.numfiles, max=self.numfiles, show_time=True, can_cancel=False)
progress.open()
for idx in xrange(self.numfiles):
#pbar.update(float(idx)/self.numfiles*100)
self.CC = cv_funcs.xcorr(self.sig.data[self.tmp_img_idx,
self.top:self.top+self.tmp_size,
self.left:self.left+self.tmp_size],
self.sig.data[idx,:,:])
# peak finder needs peaks greater than 1. Multiply by 255 to scale them.
pks=pc.two_dim_findpeaks(self.CC*255, peak_width=self.peak_width, medfilt_radius=None)
pks[:,2]=pks[:,2]/255.
peaks.append(pks)
progress.update(idx+1)
#pbar.finish()
self.peaks=peaks
def retime_files(self):
if not self.gui_active:
return
chunksize = self.parent.probe_progress_chunksize
chunkcount = int(math.ceil(float(len(self.files)) / chunksize))
if chunkcount > 1:
progress = ProgressDialog(title="Images", message="Loading images", max=chunkcount, can_cancel=False, parent=self.context.uiparent)
else:
progress = gui.support.DummyProgressDialog()
progress.open()
with cache.Cache('image_metadata') as c:
for i, f in enumerate(self.files):
if i % chunksize == 0:
progress.update(i / chunksize)
f.timestamp, f.exposure = self.get_timestamp(c, i, f.path)
self.files = self.sort_files(self.files)
progress.update(progress.max)
progress.close()
def get_files(self, reload=False):
chunksize = self.parent.probe_progress_chunksize
if reload or not self.files:
filenames = glob.glob(os.path.join(self.directory, self.pattern))
chunkcount = int(math.ceil(float(len(filenames)) / chunksize))
if chunkcount > 1:
progress = ProgressDialog(title="Images", message="Loading images", max=chunkcount, can_cancel=False, parent=self.parent.context.uiparent)
else:
progress = gui.support.DummyProgressDialog()
files = []
with cache.Cache('image_metadata') as c:
progress.open()
for i in range(chunkcount):
eiter = enumerate(filenames[chunksize*i:chunksize*(i+1)], chunksize*i)
files.extend(ImageFile.probefile(files, c, i, fn, self.get_timestamp) for (i, fn) in eiter)
progress.update(i)
progress.update(progress.max)
progress.close()
self.files = self.sort_files(files)
def _create_fsaverage_fired(self):
# progress dialog with indefinite progress bar
title = "Creating FsAverage ..."
message = "Copying fsaverage files ..."
prog = ProgressDialog(title=title, message=message)
prog.open()
prog.update(0)
try:
self.model.create_fsaverage()
except Exception as err:
error(None, str(err), "Error Creating FsAverage")
raise
finally:
prog.close()
def task_func(t):
progress = ProgressDialog(title="progress", message="counting to %d"%t, max=t, show_time=True, can_cancel=True)
progress.open()
for i in range(0,t+1):
time.sleep(1)
print(i)
(cont, skip) = progress.update(i)
if not cont or skip:
break
progress.update(t)
def task_func(t):
progress = ProgressDialog(title="progress",
message="counting to %d" % t,
max=t,
show_time=True,
can_cancel=True)
progress.open()
for i in range(0, t + 1):
time.sleep(1)
print(i)
(cont, skip) = progress.update(i)
if not cont or skip:
break
progress.update(t)
def _get_misc_data(self):
if not self.raw:
return
if self.show_gui:
# progress dialog with indefinite progress bar
prog = ProgressDialog(title="Loading SQD data...",
message="Loading stim channel data from SQD "
"file ...")
prog.open()
prog.update(0)
else:
prog = None
try:
data, times = self.raw[self.misc_chs]
except Exception as err:
if self.show_gui:
error(None, str(err), "Error Creating FsAverage")
raise
finally:
if self.show_gui:
prog.close()
return data
def run_model(self, modeldata):
self.simulation = True
self.md = modeldata
self.c_stock = numpy.empty(shape=(0, 10), dtype=numpy.float32)
self.c_change = numpy.empty(shape=(0, 10), dtype=numpy.float32)
self.co2_yield = numpy.empty(shape=(0, 3), dtype=numpy.float32)
self.timemap = defaultdict(list)
self.area_timemap = defaultdict(list)
samplesize = self.md.sample_size
msg = "Simulating %d samples for %d timesteps" % (
samplesize, self.md.simulation_length)
progress = ProgressDialog(title="Simulation",
message=msg,
max=samplesize,
show_time=True,
can_cancel=True)
progress.open()
timesteps = self.md.simulation_length
self.timestep_length = self.md.timestep_length
self.ml_run = True
self.infall = {}
self.initial_mode = self.md.initial_mode
if self.initial_mode == 'steady state':
self.initial_def = self.md.steady_state
else:
self.initial_def = self.md.initial_litter
timemsg = None
for j in range(samplesize):
(cont, skip) = progress.update(j)
if not cont or skip:
break
self.draw = True
self.curr_yr_ind = 0
self.curr_month_ind = 0
for k in range(timesteps):
self._predict_timestep(j, k)
self.ml_run = False
self._fill_moment_results()
progress.update(samplesize)
if timemsg is not None:
error(timemsg, title='Error handling timesteps', buttons=['OK'])
return self.c_stock, self.c_change, self.co2_yield
def _render_animation_fired(self):
self.stop = True
n_frames_render = self.render_to_frame - self.render_from_frame
# prepare the render window
renwin = self._figure.scene.render_window
aa_frames = renwin.aa_frames
renwin.aa_frames = 8
renwin.alpha_bit_planes = 1
# turn on off screen rendering
#renwin.off_screen_rendering = True
# set size of window
if self.fix_image_size:
orig_size = renwin.size
renwin.size = self.image_size
# render the frames
progress = ProgressDialog(title="Rendering", max=n_frames_render,
show_time=True, can_cancel=True)
progress.open()
self.is_rendering_animation = True
for frame in range(self.render_from_frame, self.render_to_frame + 1):
# move animation to desired frame, this will also render the scene
self.current_frame = frame
# prepare window to image writer
render = tvtk.WindowToImageFilter(input=renwin, magnification=1)#, input_buffer_type='rgba')
if not self.fix_image_size:
render.magnification = self.magnification
exporter = tvtk.PNGWriter(file_name=path.join(self.render_directory, self.render_name_pattern % frame))
configure_input(exporter,render)
exporter.write()
do_continue, skip = progress.update(frame - self.render_from_frame)
if not do_continue:
break
# reset the render window to old values
renwin.aa_frames = aa_frames
if self.fix_image_size:
renwin.size = orig_size
#renwin.off_screen_rendering = False
self.is_rendering_animation = False
progress.close()
def _get_misc_data(self):
if not self.raw:
return
if self.show_gui:
# progress dialog with indefinite progress bar
prog = ProgressDialog(title="Loading SQD data...",
message="Loading stim channel data from SQD "
"file ...")
prog.open()
prog.update(0)
else:
prog = None
try:
data, times = self.raw[self.misc_chs]
except Exception as err:
if self.show_gui:
error(None, str(err), "Error Creating FsAverage")
raise err
finally:
if self.show_gui:
prog.close()
return data
def run_model(self, modeldata):
self.simulation = True
self.md = modeldata
self.c_stock = numpy.empty(shape=(0,10), dtype=numpy.float32)
self.c_change = numpy.empty(shape=(0,10), dtype=numpy.float32)
self.co2_yield = numpy.empty(shape=(0,3), dtype=numpy.float32)
self.timemap = defaultdict(list)
self.area_timemap = defaultdict(list)
samplesize = self.md.sample_size
msg = "Simulating %d samples for %d timesteps" % (samplesize,
self.md.simulation_length)
progress = ProgressDialog(title="Simulation", message=msg,
max=samplesize, show_time=True,
can_cancel=True)
progress.open()
timesteps = self.md.simulation_length
self.timestep_length = self.md.timestep_length
self.ml_run = True
self.infall = {}
self.initial_mode = self.md.initial_mode
if self.initial_mode=='steady state':
self.initial_def = self.md.steady_state
else:
self.initial_def = self.md.initial_litter
timemsg = None
for j in range(samplesize):
(cont, skip) = progress.update(j)
if not cont or skip:
break
self.draw = True
self.curr_yr_ind = 0
self.curr_month_ind = 0
for k in range(timesteps):
self._predict_timestep(j, k)
self.ml_run = False
self._fill_moment_results()
progress.update(samplesize)
if timemsg is not None:
error(timemsg, title='Error handling timesteps',
buttons=['OK'])
return self.c_stock, self.c_change, self.co2_yield
def __getitem__(self, factor_slices):
'''
Access to the output_array using factor level indices.
This method enables access to the values using the syntax
output_sub_array = pstudy[ f1_level_idx, f2_level_idx, ... ]
Here the standard numpy indices including slice and elipses can be used.
'''
# map the slices within the levels2run array
# to the indices of the expanded input_table
#
n_sims = self._get_slice_n_sims(factor_slices)
progress = ProgressDialog(title='simulation progress',
message='running %d simulations' % n_sims,
max=n_sims,
show_time=True,
can_cancel=True)
progress.open()
run_idx_list = self.levels2run[factor_slices].flatten()
runs_levels = self.input_table[run_idx_list]
runs_levels_idx = self.run2levels[run_idx_list]
# start the computation for each of the runs
#
sim_idx = 0
for run_levels, run_levels_idx in zip(runs_levels, runs_levels_idx):
# check to see if this run is already in the cache
#
outputs = self._output_cache.get(tuple(run_levels), None)
if outputs == None:
print 'new simulation', sim_idx
# Set the factor values of the run in
# the simulation model
#
for factor_name, factor, level in zip(self.factor_names,
self.factor_list,
run_levels):
level = factor.get_level_value(level)
setattr(self.sim_model, factor_name, level)
# Perform the simulation
#
outputs = self.sim_model.peval()
self.output_array[tuple(run_levels_idx)] = outputs
self._output_cache[tuple(run_levels)] = outputs
else:
print 'cached simulation', sim_idx
# let the progress bar interfere
#
(cont, skip) = progress.update(sim_idx)
if not cont or skip:
break
sim_idx += 1
progress.update(n_sims)
return self.output_array[factor_slices]
def read_data(self):
""" Obtain x_locations, y_locations, data_locations, traces in a context
Returns:
---------
context: DataContext
"""
# Check if the filename is valid for reading data
if not self.file_handle:
return None
# Set the file reader at the first char.
if self.file_handle.closed:
self.file_handle = file(self.filename, 'rb')
# Setup a progress dialog
progress = ProgressDialog(title='Reading Segy Files',
message='Reading Segy Files',
max=100, show_time=True, can_cancel=True)
progress.open()
# Skip the card_image_header and binary header
self.file_handle.seek(Segy.CARD_IMAGE_HEADER_LEN +
Segy.BINARY_HEADER_LEN)
progress.update(1)
# Check if data lengths are correct.
x_data_len = struct.calcsize(self.x_format)
y_data_len = struct.calcsize(self.y_format)
inline_data_len = struct.calcsize(self.inline_format)
crossline_data_len = struct.calcsize(self.crossline_format)
if not (x_data_len == y_data_len and
y_data_len == inline_data_len and
inline_data_len == crossline_data_len):
logger.error('SegyReader: Mismatch in format lengths')
return None
if self.scale_format != '':
scale_data_len = struct.calcsize(self.scale_format)
if scale_data_len != x_data_len:
logger.error('SegyReader: Mismatch in format lengths')
return None
# Get trace header data of 240 bytes.
header_data = self.file_handle.read(Segy.TRACE_HEADER_LEN)
traces, read_error = [], False
previous_update = 1
while header_data != '' and not read_error:
trace = self._read_trace(header_data, x_data_len)
if trace is None:
logger.error('SegyReader: Error in reading a trace')
read_error = True
else:
traces.append(trace)
header_data = self.file_handle.read(Segy.TRACE_HEADER_LEN)
progress_pc = 1 + int(98.0*float(len(traces))/
float(self.trace_count))
if progress_pc - previous_update > 1:
cont_val, skip_val = progress.update(progress_pc)
previous_update = progress_pc
# If the user has cancelled the action then stop the import
# immediately
if skip_val or not cont_val:
del traces
self.file_handle.close()
return None
self.file_handle.close()
progress.update(100)
if read_error:
del traces
return None
else:
arr_descriptor = {'names': ('x','y','inline','crossline',
'scale_factor', 'trace'),
'formats': ('f4', 'f4', 'f4', 'f4', 'f4',
str(self.samples_per_trace)+'f4')
}
traces = array(traces, dtype=arr_descriptor)
filesplit = os.path.split(self.filename)
name = str(os.path.splitext(filesplit[1])[0]).translate(trans_table)
return DataContext(
name=name,
_bindings={'traces':traces['trace'],
'x_locations':traces['x'],
'y_locations':traces['y'],
'inline_values':traces['inline'],
'crossline_values':traces['crossline'],
'scale_factors':traces['scale_factor']})
return
def __getitem__(self, factor_slices):
'''
Access to the output_array using factor level indices.
This method enables access to the values using the syntax
output_sub_array = pstudy[ f1_level_idx, f2_level_idx, ... ]
Here the standard numpy indices including slice and elipses can be used.
'''
# map the slices within the levels2run array
# to the indices of the expanded input_table
#
n_sims = self._get_slice_n_sims(factor_slices)
progress = ProgressDialog(title='simulation progress',
message='running %d simulations' % n_sims,
max=n_sims,
show_time=True,
can_cancel=True)
progress.open()
run_idx_list = self.levels2run[factor_slices].flatten()
runs_levels = self.input_table[run_idx_list]
runs_levels_idx = self.run2levels[run_idx_list]
# start the computation for each of the runs
#
sim_idx = 0
for run_levels, run_levels_idx in zip(runs_levels, runs_levels_idx):
# check to see if this run is already in the cache
#
outputs = self._output_cache.get(tuple(run_levels), None)
if outputs == None:
print 'new simulation', sim_idx
# Set the factor values of the run in
# the simulation model
#
for factor_name, factor, level in zip(self.factor_names,
self.factor_list,
run_levels):
level = factor.get_level_value(level)
setattr(self.sim_model, factor_name, level)
# Perform the simulation
#
outputs = self.sim_model.peval()
self.output_array[tuple(run_levels_idx)] = outputs
self._output_cache[tuple(run_levels)] = outputs
else:
print 'cached simulation', sim_idx
# let the progress bar interfere
#
(cont, skip) = progress.update(sim_idx)
if not cont or skip:
break
sim_idx += 1
progress.update(n_sims)
return self.output_array[factor_slices]
def characterize(self, target_locations=None,
target_neighborhood=20,
medfilt_radius=5):
#print "Main thread?"
#print Application.instance().is_main_thread()
# disable the UI while we're running
self._toggle_UI(False)
#print
try:
# wipe out old results
self.chest.removeNode('/cell_peaks')
except:
# any errors will be because the table doesn't exist. That's OK.
pass
# locate peaks on the average image to use as target locations.
# also determines the number of peaks, which in turn determines
# the table columns.
target_locations = pc.two_dim_findpeaks(self._get_average_image(),
)[:,:2]
self.numpeaks = int(target_locations.shape[0])
# generate a list of column names
names = [('x%i, y%i, dx%i, dy%i, h%i, o%i, e%i, sx%i, sy%i' % ((x,)*9)).split(', ')
for x in xrange(self.numpeaks)]
# flatten that from a list of lists to a simple list
names = [item for sublist in names for item in sublist]
# make tuples of each column name and 'f8' for the data type
dtypes = zip(names, ['f8', ] * self.numpeaks*9)
# prepend the filename and index columns
dtypes = [('filename', '|S250'), ('file_idx', 'i4'), ('omit', 'bool')] + dtypes
# create an empty recarray with our data type
desc = np.recarray((0,), dtype=dtypes)
# create the table using the empty description recarray
self.chest.createTable(self.chest.root,
'cell_peaks', description=desc)
# for each file in the cell_data group, run analysis.
nodes = self.chest.listNodes('/cells')
node_names = [node.name for node in nodes]
progress = ProgressDialog(title="Peak characterization progress",
message="Characterizing peaks on %d images"%(len(node_names)-2),
max=len(node_names)-1, show_time=True, can_cancel=False)
progress.open()
file_progress=0
for node in node_names:
# exclude some nodes
if node == 'template':
continue
cell_data = self.get_cell_set(node)
data = np.zeros((cell_data.shape[0]),dtype=dtypes)
data['filename'] = node
data['file_idx'] = np.arange(cell_data.shape[0])
# might want to tweak this loop or cythonize for speed...
attribs = self._peak_attribs_stack(cell_data,
peak_width=self.peak_width,
target_locations=target_locations,
target_neighborhood=target_neighborhood,
medfilt_radius=medfilt_radius)
attribs = attribs.T
# for each column name, copy in the data
for name_idx in xrange(len(names)):
data[names[name_idx]] = attribs[:, name_idx]
# add the data to the table
self.chest.root.cell_peaks.append(data)
self.chest.root.cell_peaks.flush()
file_progress+=1
progress.update(file_progress)
# add an attribute for the total number of peaks recorded
self.chest.setNodeAttr('/cell_peaks','number_of_peaks', self.numpeaks)
self.chest.root.cell_peaks.flush()
self.chest.flush()
self._can_show_peak_ids = True
self.parent.image_controller.update_peak_map_choices()
self._progress_value = 0
self.log_action(action="Characterize peaks",
target_locations=target_locations,
target_neighborhood=target_neighborhood,
medfilt_radius=medfilt_radius)
self._toggle_UI(True)
def do_export_movie(self, info):
context = info.ui.context['object'].context
moviedialog = context.app.export_movie_dialog
try:
if not moviedialog.run().result:
return
except RuntimeError as e:
support.Message.show(parent=context.uiparent, message='Nothing to animate', desc=str(e))
return
dlg = wx.FileDialog(
info.ui.control,
"Save movie",
context.prefs.get_path('export_movie'),
"movie." + moviedialog.format,
"*.{0}|*.{0}|All files (*.*)|*.*".format(moviedialog.format),
wx.SAVE|wx.OVERWRITE_PROMPT
)
if dlg.ShowModal() != wx.ID_OK:
return
context.prefs.set_path('export_movie', dlg.GetDirectory())
# preparations, no harm is done if something goes wrong here
movie = stdout_cb = stdout = None
oldfig = context.plot.figure
progress = ProgressDialog(title="Movie", message="Building movie", max=moviedialog.get_framecount()+2, can_cancel=True, show_time=True, parent=context.uiparent)
newfig = matplotlib.figure.Figure((moviedialog.frame_width / moviedialog.dpi, moviedialog.frame_height / moviedialog.dpi), moviedialog.dpi)
canvas = FigureCanvasAgg(newfig)
drawmgr = context.canvas.relocate(redraw=newfig.canvas.draw)
finalpath = dlg.GetPath()
if '%' in finalpath: # to support stuff like -f image2 -c:v png file_%02.png
temppath = False
else:
temppath = finalpath + '.temp'
class UserCanceled(Exception): pass
class FFmpegFailed(Exception): pass
# now the real thing starts. we have to clean up properly
try:
progress.open()
context.plot.relocate(newfig)
movie = util.FFmpegEncode(
temppath or finalpath,
moviedialog.format,
moviedialog.codec,
moviedialog.frame_rate,
(moviedialog.frame_width, moviedialog.frame_height),
moviedialog.ffmpeg_options.split(),
)
stdout_cb = movie.spawnstdoutthread()
drawmgr.rebuild()
progress.update(1)
iters = tuple(i() for i in moviedialog.get_animate_functions())
frameiter = enumerate(itertools.izip_longest(*iters))
while True:
with drawmgr.hold():
try:
frameno, void = frameiter.next()
except StopIteration:
progress.update(progress.max-1)
break
movie.writeframe(newfig.canvas.tostring_rgb())
(cont, skip) = progress.update(frameno+2)
if not cont or skip:
raise UserCanceled()
ret = movie.close()
if ret != 0:
raise FFmpegFailed('ffmpeg returned {0}'.format(ret))
stdout = stdout_cb()
stdout_cb = None
if temppath:
shutil.move(temppath, finalpath)
progress.update(progress.max)
except UserCanceled:
movie.abort()
return
except:
if movie:
movie.close()
if stdout_cb:
try:
stdout = stdout_cb()
except:
pass
stdout_cb = None
support.Message.show(
parent=context.uiparent,
message='Movie export failed', title='Exception occured',
desc='Something went wrong while exporting the movie. Detailed debugging information can be found below.',
bt="FFMPEG output:\n{0}\n\nBACKTRACE:\n{1}".format(stdout, traceback.format_exc())
)
return
finally:
if stdout_cb:
stdout = stdout_cb()
progress.close()
try:
os.remove(temppath)
except:
pass
context.plot.relocate(oldfig)
context.canvas.rebuild()
support.Message.show(
parent=context.uiparent,
title='Movie complete', message='Movie complete',
desc='The movie successfully been generated.\nFor debugging purposes, the full FFmpeg output can be found below.',
bt=stdout
)
def read_data(self):
""" Obtain x_locations, y_locations, data_locations, traces in a context
Returns:
---------
context: DataContext
"""
# Check if the filename is valid for reading data
if not self.file_handle:
return None
# Set the file reader at the first char.
if self.file_handle.closed:
self.file_handle = file(self.filename, 'rb')
# Setup a progress dialog
progress = ProgressDialog(title='Reading Segy Files',
message='Reading Segy Files',
max=100,
show_time=True,
can_cancel=True)
progress.open()
# Skip the card_image_header and binary header
self.file_handle.seek(Segy.CARD_IMAGE_HEADER_LEN +
Segy.BINARY_HEADER_LEN)
progress.update(1)
# Check if data lengths are correct.
x_data_len = struct.calcsize(self.x_format)
y_data_len = struct.calcsize(self.y_format)
inline_data_len = struct.calcsize(self.inline_format)
crossline_data_len = struct.calcsize(self.crossline_format)
if not (x_data_len == y_data_len and y_data_len == inline_data_len
and inline_data_len == crossline_data_len):
logger.error('SegyReader: Mismatch in format lengths')
return None
if self.scale_format != '':
scale_data_len = struct.calcsize(self.scale_format)
if scale_data_len != x_data_len:
logger.error('SegyReader: Mismatch in format lengths')
return None
# Get trace header data of 240 bytes.
header_data = self.file_handle.read(Segy.TRACE_HEADER_LEN)
traces, read_error = [], False
previous_update = 1
while header_data != '' and not read_error:
trace = self._read_trace(header_data, x_data_len)
if trace is None:
logger.error('SegyReader: Error in reading a trace')
read_error = True
else:
traces.append(trace)
header_data = self.file_handle.read(Segy.TRACE_HEADER_LEN)
progress_pc = 1 + int(
98.0 * float(len(traces)) / float(self.trace_count))
if progress_pc - previous_update > 1:
cont_val, skip_val = progress.update(progress_pc)
previous_update = progress_pc
# If the user has cancelled the action then stop the import
# immediately
if skip_val or not cont_val:
del traces
self.file_handle.close()
return None
self.file_handle.close()
progress.update(100)
if read_error:
del traces
return None
else:
arr_descriptor = {
'names':
('x', 'y', 'inline', 'crossline', 'scale_factor', 'trace'),
'formats': ('f4', 'f4', 'f4', 'f4', 'f4',
str(self.samples_per_trace) + 'f4')
}
traces = array(traces, dtype=arr_descriptor)
filesplit = os.path.split(self.filename)
name = str(os.path.splitext(
filesplit[1])[0]).translate(trans_table)
return DataContext(name=name,
_bindings={
'traces': traces['trace'],
'x_locations': traces['x'],
'y_locations': traces['y'],
'inline_values': traces['inline'],
'crossline_values': traces['crossline'],
'scale_factors': traces['scale_factor']
})
return
def initialize(self, title, max_index):
self.progress = ProgressDialog(title="Characterizing %d peaks on current image"%max_index,
max=int(max_index), show_time=True, can_cancel=False)
self.progress.open()
def _progress_dialog_default(self):
return ProgressDialog(
min=0,
max=100,
)
def _peak_attribs_stack(self, stack, peak_width, target_locations=None,
target_neighborhood=20, medfilt_radius=5,
mask = True):
"""
Characterizes the peaks in a stack of images.
Parameters:
----------
peak_width : int (required)
expected peak width. Too big, and you'll include other peaks
in measurements.
target_locations : numpy array (n x 2)
array of n target locations. If left as None, will create
target locations by locating peaks on the average image of the stack.
default is None (peaks detected from average image)
img_size : tuple, 2 elements
(width, height) of images in image stack.
target_neighborhood : int
pixel neighborhood to limit peak search to. Peaks outside the
square defined by 2x this value around the peak will be excluded
from any fitting.
medfilt_radius : int (optional)
median filter window to apply to smooth the data
(see scipy.signal.medfilt)
if 0, no filter will be applied.
default is set to 5
Returns:
-------
2D numpy array:
- One column per image
- 9 rows per peak located
0,1 - location
2,3 - difference between location and target location
4 - height
5 - orientation
6 - eccentricity
7,8 - skew X, Y, respectively
"""
avgImage=np.average(stack,axis=0)
if target_locations is None:
# get peak locations from the average image
# an initial value for the peak width of 11 pixels works
# OK to find initial peaks. We determine a proper value
# soon.
target_locations=pc.two_dim_findpeaks(avgImage, 10)
peak_width = 0.75*pc.min_peak_distance(target_locations)
if peak_width < 10:
peak_width = 10
if mask:
mask = pc.draw_mask(avgImage.shape,
peak_width/2.0,
target_locations)
stack *= mask
# get all peaks on all images
peaks=pc.stack_coords(stack, peak_width=peak_width)
# two loops here - outer loop loops over images (i index)
# inner loop loops over target peak locations (j index)
peak_locations=np.array([[pc.best_match(peaks[:,:,i],
target_locations[j,:2],
target_neighborhood) \
for i in xrange(peaks.shape[2])] \
for j in xrange(target_locations.shape[0])])
# pre-allocate result array. 7 rows for each peak, 1 column for each image
rlt = np.zeros((9*peak_locations.shape[0],stack.shape[0]))
rlt_tmp = np.zeros((peak_locations.shape[0],7))
progress = ProgressDialog(title="Peak characterization progress",
message="Characterizing peaks on %d cells"%stack.shape[0],
max=int(stack.shape[0]), show_time=True, can_cancel=False)
progress.open()
for i in xrange(stack.shape[0]):
progress.update(int(i+1))
rlt_tmp=pc.peak_attribs_image(stack[i,:,:],
target_locations=peak_locations[:,i,:],
peak_width=peak_width,
medfilt_radius=medfilt_radius,
)
diff_coords=target_locations[:,:2]-rlt_tmp[:,:2]
for j in xrange(target_locations.shape[0]):
# peak position
rlt[ j*9 : j*9+2 ,i] = rlt_tmp[j,:2]
# difference in peak position relative to average
rlt[ j*9+2 : j*9+4 ,i] = diff_coords[j]
# height
rlt[ j*9+4 ,i]=rlt_tmp[j,2]
# orientation
rlt[ j*9+5 ,i]=rlt_tmp[j,3]
# eccentricity
rlt[ j*9+6 ,i]=rlt_tmp[j,4]
# skew (x and y)
rlt[ j*9+7 : j*9+9 ,i]=rlt_tmp[j,5:]
return rlt
def peak_attribs_image(image, peak_width=None, target_locations=None, medfilt_radius=5):
"""
Characterizes the peaks in an image.
Parameters:
----------
peak_width : int (optional)
expected peak width. Affects characteristic fitting window.
Too big, and you'll include other peaks in the measurement.
Too small, and you'll get spurious peaks around your peaks.
Default is None (attempts to auto-detect)
target_locations : numpy array (n x 2)
array of n target locations. If left as None, will create
target locations by locating peaks on the average image of the stack.
default is None (peaks detected from average image)
medfilt_radius : int (optional)
median filter window to apply to smooth the data
(see scipy.signal.medfilt)
if 0, no filter will be applied.
default is set to 5
Returns:
-------
2D numpy array:
- One row per peak
- 7 columns:
0,1 - location
2 - height
3,4 - long and short axis length
5 - orientation
6 - eccentricity
7,8 - skew
"""
try:
import cv
except:
try:
import cv2.cv as cv
except:
print 'Module %s:' % sys.modules[__name__]
print 'OpenCV is not available, the peak characterization functions will not work.'
return None
if medfilt_radius:
image=medfilt(image,medfilt_radius)
if target_locations is None:
# target locations should be a list of arrays. Each element in the
# list corresponds to a recursion level in peak finding. The peak
# width can change with each recursion.
target_locations=two_dim_findpeaks(image, peak_width=peak_width, medfilt_radius=5,coords_list=[])
imsize=image.shape[0]
total_peaks = np.array([arr.shape[0] for arr in target_locations]).sum()
rlt=np.zeros((total_peaks,9))
# TODO: this should be abstracted to use whatever graphical
# or command-line environment we're in.
progress = ProgressDialog(title="Peak characterization progress",
message="Characterizing %d peaks on current image"%total_peaks,
max=int(total_peaks), show_time=True, can_cancel=False)
progress.open()
rlt_offset=0
progress_ctr=0
for recursed_peak_array in target_locations:
peak_width = recursed_peak_array[0][3]
r=np.ceil(peak_width/2)
roi=np.zeros((r*2,r*2))
mask = draw_mask((r*2,r*2), r, [(r,r)])
for loc in xrange(recursed_peak_array.shape[0]):
c=recursed_peak_array[loc]
peak_left=c[0]-r
peak_top=c[1]-r
peak_right=c[0]+r
peak_bottom=c[1]+r
#if bxmin<0: bxmin=0; bxmax=peak_width
#if bymin<0: bymin=0; bymax=peak_width
#if bxmax>imsize: bxmax=imsize; bxmin=imsize-peak_width
#if bymax>imsize: bymax=imsize; bymin=imsize-peak_width
# skip peaks that are too close to edges.
if (peak_right)>image.shape[1]+r/4 or (peak_bottom)>image.shape[0]+r/4:
progress_ctr+=1
continue
# set the neighborhood of the peak to zero so we go look elsewhere
# for other peaks
x = np.array(np.arange(peak_left, peak_right),dtype=np.integer)
y = np.array(np.arange(peak_top, peak_bottom),dtype=np.integer)
xv,yv = np.meshgrid(x,y)
roi[:,:] = image[yv.clip(0,image.shape[0]-1),
xv.clip(0,image.shape[1]-1)] * mask
#roi[0:,:]=image[bymin:bymax,bxmin:bxmax]
# skip frames with significant dead pixels (corners of
# rotated images, perhaps
#if np.average(roi)< 0.5*np.average(image):
#rlt[loc,:2] = (c[1], c[0])
#continue
ms=cv.Moments(cv.fromarray(roi))
# output from get_characteristics is:
# x, y, height, long_axis, short_axis, orientation, eccentricity, skew_x, skew_y
rlt[rlt_offset] = get_characteristics(ms)
# order for these is:
# amp, xShift, yShift, xWidth, height, yWidth, Rotation
# WTF??? Why is this different from return order!?
# I'm a control freak...
limit_min = [True, True, True, True, True, True, True]
limit_max = [True, True, True, True, True, True, True]
# 30 pixels seems like a hell of a lot for a peak...
max_width=30
max_height = 1.2*np.max(roi)
ctr = np.array(roi.shape)/2
min_height = np.mean(image)/1.5
x = rlt[rlt_offset][0]
y = rlt[rlt_offset][1]
amp = image[peak_top+y,peak_left+x]
long_axis = rlt[rlt_offset][3]
short_axis = rlt[rlt_offset][4]
orientation = rlt[rlt_offset][5]
height = 0
params = [amp, x, y, long_axis, height, short_axis, orientation]
minpars = [min_height, x-2, y-2, 0, 0, 0, 0]
maxpars = [max_height, x+2, y+2, max_width, 0, max_width, 360]
# TODO: could use existing moments or parameters to speed up...
amp, fit_x, fit_y, width_x, height, width_y, rot = gaussfit(roi,
limitedmin=limit_min,
limitedmax=limit_max,
maxpars=maxpars,
minpars=minpars,
params=params
)
# x and y are the locations within the ROI. Add the coordinates of
# the top-left corner of our ROI on the global image.
rlt[rlt_offset,:2] = (np.array([peak_top,peak_left]) + np.array([fit_y,fit_x]))
#rlt[loc,:2] = np.array([y,x])
# insert the height
rlt[rlt_offset,2]=amp+height
# TODO: compare this with OpenCV moment calculation above:
# (this is using the gaussfitter value)
rlt[rlt_offset,5]=rot
rlt_offset+=1
progress_ctr+=1
progress.update(int(progress_ctr))
# chuck outliers based on median of height
d = np.abs(rlt[:,2] - np.median(rlt[:,2]))
mdev = np.median(d)
s = d/mdev if mdev else 0
# kill outliers based on height
rlt=rlt[np.logical_and(s<10, rlt[:,2]<image.max()*1.3)]
# kill peaks that are too close to other peaks
# the minimum width is 1.5 times the smallest peak width.
min_width = 1.5*target_locations[-1][0][3]
#rlt = kill_duplicates(rlt,min_width)
return rlt