def __init__(self, rw):
self.rw = rw
self.rw_warp = ris_widget.RisWidget()
self.layout = Qt.QFormLayout()
spline_widget = Qt.QWidget()
spline_widget.setLayout(self.layout)
self.warp = Qt.QPushButton("Warp Worm")
self.clear = Qt.QPushButton("Clear")
self.layout.addRow(self.warp)
self.rw.flipbook.layout().addWidget(spline_widget)
self.warp.clicked.connect(self._on_warp_clicked)
def main(argv=None):
import argparse
parser = argparse.ArgumentParser(description='straighten worm images')
parser.add_argument('pixels_per_micron', nargs='?', default=1/1.3, type=float, metavar='pixels_per_micron', help='conversion factor for objective used')
parser.add_argument('images', nargs="*", metavar='image', help='image files to open')
args = parser.parse_args(argv)
rw = ris_widget.RisWidget()
gp = GeneralPoseAnnotator(rw, pixels_per_micron=args.pixels_per_micron)
rw.add_image_files_to_flipbook(args.images)
rw.run()
def __init__(self,
in_dir,
image_glob,
labels,
autosave_dir=None,
start_idx=0,
stop_idx=None):
self.rw = ris_widget.RisWidget()
self._init_notefield()
if type(autosave_dir) is str:
self.autosave_dir = pathlib.Path(autosave_dir)
else:
self.autosave_dir = autosave_dir
self.in_dir = in_dir
self.labels = labels
self.image_glob = image_glob
self.start_idx = start_idx
self.stop_idx = stop_idx
self.all_images, self.worm_positions = self.parse_inputs()
#self.dictionary=dict.fromkeys(self.worm_positions)
#for key, entry in self.dictionary.items():
#self.dictionary[key]=dict.fromkeys(labels)
self.worm_info = pd.DataFrame(index=self.worm_positions,
columns=self.labels +
['Notes']) # Add extra field for notes
self.set_index(0)
self.actions = []
#self._add_action('left', Qt.Qt.Key_Left, lambda: self.load_next_worm(self.well_index,-1))
#self._add_action('right', Qt.Qt.Key_Right, lambda: self.load_next_worm(self.well_index,1))
self._add_action(
'prev', Qt.Qt.Key_BracketLeft,
lambda: self.load_next_worm(self.well_index, -1)
) # Changed these because I tended to accidentally hit side keys
self._add_action('next', Qt.Qt.Key_BracketRight,
lambda: self.load_next_worm(self.well_index, 1))
self._add_action('Save Annotations', QtGui.QKeySequence('Ctrl+S'),
self.save_annotations)
self.rw.qt_object.main_view_toolbar.addAction(self.actions[-1])
self._add_action('Load Annotations', QtGui.QKeySequence('Ctrl+O'),
self.load_annotations)
self.rw.qt_object.main_view_toolbar.addAction(self.actions[-1])
self._add_action('Goto Index', QtGui.QKeySequence('Ctrl+G'),
self.goto_index)
self.rw.qt_object.main_view_toolbar.addAction(self.actions[-1])
self.rw.show()
experiment_dir = pathlib.Path(
'/mnt/9karray/Sinha_Drew/20180518_spe-9_Run_3/')
timepoint = '2018-05-22t1716' # Early timepoint
timepoint = '2018-05-28t1710' # Late timepoint ~8d - eggs are super autofluorescent!!!!! churned up food doesn't help either....
experiment_dir = pathlib.Path(
'/mnt/9karray/Sinha_Drew/20180524_spe-9_Run_4/')
timepoint = '2018-05-28t1526' # Early timepoint
timepoint = '2018-06-03t1714' # Late timepoint ~8d ..
if view_files:
try:
rw
except NameError:
rw = ris_widget.RisWidget()
rw.show()
def timepoint_filter(position_name, timepoint_name):
return timepoint_name == timepoint
experiment_images = load_data.scan_experiment_dir(
experiment_dir,
timepoint_filter=timepoint_filter,
channels=['bf', 'green_yellow_excitation_autofluorescence'])
image_names, images = [], []
fl_image_modes = [] # Measurement of the gel
fl_image_center_medians = [
] # Measurement of the food (1100,900) to (1300, 1100)
for position_name, position_images in experiment_images.items():
def make_global_riswidget():
rw_defined = 'rw' in globals()
global rw
if not rw_defined:
rw = ris_widget.RisWidget()
return rw
show_masks = False
readonly = True
annotation_dir = 'annotations'
# optional filters to eliminate relevant position/timepoints
timepoint_filters = [
load_data.filter_excluded
] #, elegant_filters.filter_live_animals] #, elegant_filters.filter_after_timepoint('2019-05-20t0000')] #, elegant_filters.select_worms(['15']), elegant_filters.filter_live_animals, elegant_filters.filter_by_stage('adult')] #, elegant_filters.filter_after_timepoint('2019-02-02t1200')]
channels = [
'bf'
] #, 'gfp'] #, 'autofluorescence'] #, 'green_yellow_excitation_autofluorescence'] # First one is the one used to load poses when specified.
# Only use one RisWidget for annotations
rw_defined = 'rw' in globals()
global rw
if not rw_defined: rw = ris_widget.RisWidget()
# Allows one to restart annotating in the same ris_widget window
if hasattr(rw, 'annotator'):
rw.annotator.close()
del (rw.annotator)
process_data.update_annotations(expt_dir)
experiment_annotations = load_data.read_annotations(
expt_dir, annotation_dir=annotation_dir)
if timepoint_filters:
experiment_annotations = load_data.filter_annotations(
experiment_annotations,
elegant_filters.compose_timepoint_filters(*timepoint_filters))