def image_meta(self, filescanner, patterns=('*', )):
def fnmatch_any(fname, patterns):
return any(
fnmatch.fnmatch(
fname.lower() if self.case_insensitive else fname, pattern)
for pattern in patterns)
imgmeta = []
batch = []
for path in filescanner:
if fnmatch_any(path, patterns):
imeta = image_meta_data(path)
imgmeta.append(imeta)
batch.append(imgmeta)
if self.cancelled:
return
# raise UserInterruptError
if len(batch) == 10 and self.report_progress is not None:
self.report_progress(
namespace(count=len(imgmeta),
lastpath=imgmeta[-1].path,
batch=batch))
batch = []
if batch and self.report_progress is not None:
self.report_progress(
namespace(count=len(imgmeta),
lastpath=imgmeta[-1].path,
batch=batch))
return imgmeta
def run(self):
imgmeta = []
filescanner = scan(self.startdir)
patterns = ["*.{}".format(fmt.lower()) for fmt in self.formats]
def fnmatch_any(fname, patterns):
return any(fnmatch.fnmatch(fname.lower(), pattern)
for pattern in patterns)
batch = []
for path in filescanner:
if fnmatch_any(path, patterns):
imeta = image_meta_data(path)
imgmeta.append(imeta)
batch.append(imgmeta)
if self.cancelled:
return
# raise UserInterruptError
if len(batch) == 10 and self.report_progress is not None:
self.report_progress(
namespace(count=len(imgmeta),
lastpath=imgmeta[-1].path,
batch=batch))
batch = []
if batch and self.report_progress is not None:
self.report_progress(
namespace(count=len(imgmeta),
lastpath=imgmeta[-1].path,
batch=batch))
return imgmeta
def image_meta(self, filescanner, patterns=('*', )):
def fnmatch_any(fname, patterns):
return any(fnmatch.fnmatch(fname.lower() if self.case_insensitive else fname, pattern)
for pattern in patterns)
imgmeta = []
batch = []
for path in filescanner:
if fnmatch_any(path, patterns):
imeta = image_meta_data(path)
imgmeta.append(imeta)
batch.append(imgmeta)
if self.cancelled:
return
# raise UserInterruptError
if len(batch) == 10 and self.report_progress is not None:
self.report_progress(
namespace(count=len(imgmeta),
lastpath=imgmeta[-1].path,
batch=batch))
batch = []
if batch and self.report_progress is not None:
self.report_progress(
namespace(count=len(imgmeta),
lastpath=imgmeta[-1].path,
batch=batch))
return imgmeta
def test_line_to_edge(self):
"""Show lint_to_edge() works as expected."""
self.challenge.lines = ['one', '1->2:12']
self.assertEqual(namespace(head=2, tail=1, weight=12),
self.challenge.line_to_edge(1))
self.challenge.lines = ['one', '1->2']
self.assertEqual(namespace(head=2, tail=1),
self.challenge.line_to_edge(1))
def _setup_plot(self):
"""Setup the plot with new curve data."""
assert self.data is not None
self.graph.reset()
data, domain = self.data, self.data.domain
self.graph.getAxis('bottom').setTicks([[
(i + 1, str(a)) for i, a in enumerate(self.graph_variables)
]])
X = np.arange(1, len(self.graph_variables) + 1)
groups = []
if not self.selected_classes:
group_data = data[:, self.graph_variables]
items, mean, meancurve, errorbar = self._plot_curve(
X, QColor(Qt.darkGray), group_data,
list(range(len(self.data))))
groups.append(
namespace(data=group_data,
profiles=items,
mean=meancurve,
boxplot=errorbar))
else:
var = domain[self.group_var]
class_col_data, _ = data.get_column_view(var)
group_indices = [
np.flatnonzero(class_col_data == i)
for i in range(len(self.classes))
]
for i, indices in enumerate(group_indices):
if len(indices) == 0:
groups.append(None)
else:
if self.classes:
color = self.class_colors[i]
else:
color = QColor(Qt.darkGray)
group_data = data[indices, self.graph_variables]
items, mean, meancurve, errorbar = self._plot_curve(
X, color, group_data, indices)
groups.append(
namespace(data=group_data,
indices=indices,
profiles=items,
mean=meancurve,
boxplot=errorbar))
self.__groups = groups
self.__update_visibility()
def preprocess(self, frame):
image_height, image_width = frame.shape[:2]
scale = min(self.h / image_height, self.w / image_width)
processed_image = cv2.resize(frame, None, fx=scale, fy=scale)
processed_image = processed_image.astype('float32').transpose(2, 0, 1)
return namespace(
original_image=frame,
meta=namespace(
original_size=frame.shape[:2],
processed_size=processed_image.shape[1:3],
),
im_data=processed_image,
im_info=np.array([processed_image.shape[1], processed_image.shape[2], 1.0], dtype='float32'),
)
def _read_text_data(self):
text_data = []
errors = []
patterns = ["*.{}".format(fmt.lower()) for fmt in self.formats]
scan = self.scan_url if self._is_url else self.scan
paths = scan(self.startdir, include_patterns=patterns)
n_paths = len(paths)
batch = []
if n_paths == 0:
raise NoDocumentsException()
for path in paths:
if len(batch) == 1 and self._report_progress is not None:
self._report_progress(
namespace(progress=len(text_data) / n_paths,
lastpath=path,
batch=batch))
batch = []
reader = Reader.get_reader(path) if not self._is_url \
else UrlReader(path)
text, error = reader.read()
if text is not None:
text_data.append(text)
batch.append(text_data)
else:
errors.append(error)
if self.cancelled:
return
return text_data, errors
def run(self):
text_data = []
errors = []
patterns = ["*.{}".format(fmt.lower()) for fmt in self.formats]
paths = self.scan(self.startdir, include_patterns=patterns)
n_paths = len(paths)
batch = []
for path in paths:
if len(batch) == 1 and self._report_progress is not None:
self._report_progress(
namespace(progress=len(text_data) / n_paths,
lastpath=path,
batch=batch))
batch = []
reader = Reader.get_reader(path)
text, error = reader.read()
if text is not None:
text_data.append(text)
batch.append(text_data)
else:
errors.append(error)
if self.cancelled:
return
self._text_data = text_data
return self._create_corpus(), errors
def info(file_path):
if file_path in allinforemote:
info = allinforemote[file_path]
else:
info = allinfolocal[file_path]
islocal = file_path in allinfolocal
isremote = file_path in allinforemote
outdated = islocal and isremote and (
allinforemote[file_path].get('version', '') !=
allinfolocal[file_path].get('version', ''))
islocal &= not outdated
prefix = os.path.join('', *file_path[:-1])
filename = file_path[-1]
return namespace(
prefix=prefix, filename=filename,
title=info.get("title", filename),
datetime=info.get("datetime", None),
description=info.get("description", None),
references=info.get("references", []),
seealso=info.get("seealso", []),
source=info.get("source", None),
year=info.get("year", None),
instances=info.get("instances", None),
variables=info.get("variables", None),
target=info.get("target", None),
missing=info.get("missing", None),
tags=info.get("tags", []),
size=info.get("size", None),
islocal=islocal,
outdated=outdated
)
def __init__(self, tfds_ds_name: str) -> None:
self._adapter = _TFDS_ADAPTERS[tfds_ds_name]
tfds_builder = tfds.builder(tfds_ds_name)
tfds_ds_info = tfds_builder.info
self._categories = {}
self._state = namespace()
self._adapter.transform_categories(tfds_builder, self._categories,
self._state)
tfds_decoders = {}
for tfds_feature_name, tfds_fc in tfds_ds_info.features.items():
if isinstance(tfds_fc, tfds.features.Image):
tfds_decoders[tfds_feature_name] = tfds.decode.SkipDecoding()
tfds_builder.download_and_prepare()
self._tfds_ds = tfds_builder.as_dataset(decoders=tfds_decoders)
self._split_extractors = {
split_name: _TfdsSplitExtractor(self, split,
tfds_ds_info.splits[split_name])
# Since dicts in Python 3.7+ (and de facto in 3.6+) are
# order-preserving, sort the splits by name so that we always
# iterate over them in alphabetical order.
for split_name, split in sorted(self._tfds_ds.items())
}
def __init__(self, obj):
# type: (Q) -> None
assert isinstance(obj, QObject)
self.__obj = obj
def finalize(_weakref):
# finalize when self is collected
if state.objref is None:
return
objref = state.objref()
if objref is not None:
objref.destroyed.disconnect(state.zero_ref)
# destroy/zero the reference when QObject is destroyed
def zero_ref():
selfref = state.selfref()
if selfref is not None:
selfref.__obj = None
state.objref = None
state = namespace(selfref=weakref.ref(self, finalize),
objref=weakref.ref(obj),
zero_ref=zero_ref,
finalize=finalize)
self.__state = state
# Must not capture self in the zero_ref's closure
obj.destroyed.connect(zero_ref, Qt.DirectConnection)
def run(self):
text_data = []
errors = []
patterns = ["*.{}".format(fmt.lower()) for fmt in self.formats]
paths = self.scan(self.startdir, include_patterns=patterns)
n_paths = len(paths)
batch = []
for path in paths:
if len(batch) == 1 and self._report_progress is not None:
self._report_progress(
namespace(progress=len(text_data) / n_paths,
lastpath=path,
batch=batch))
batch = []
reader = Reader.get_reader(path)
text, error = reader.read()
if text is not None:
text_data.append(text)
batch.append(text_data)
else:
errors.append(error)
if self.cancelled:
return
self._text_data = text_data
return self._create_corpus(), errors
def commit(self):
if self._task is not None:
self.cancel()
if not self._image_attributes or self._input_data is None:
self.clear_outputs()
return
embedder = self.connect()
_executor = concurrent.futures.ThreadPoolExecutor(max_workers=1)
self.cancel_button.setDisabled(False)
self.cb_image_attr.setDisabled(True)
self.cb_embedder.setDisabled(True)
file_paths_attr = self._image_attributes[self.cb_image_attr_current_id]
file_paths = self._input_data[:, file_paths_attr].metas.flatten()
file_paths_mask = file_paths == file_paths_attr.Unknown
file_paths_valid = file_paths[~file_paths_mask]
ticks = iter(np.linspace(0.0, 100.0, file_paths_valid.size))
set_progress = qconcurrent.methodinvoke(
self, "__progress_set", (float,))
def advance(success=True):
if success:
set_progress(next(ticks))
def cancel():
task.future.cancel()
task.cancelled = True
task.embedder.set_canceled(True)
def run_embedding():
return embedder(
self._input_data, col=file_paths_attr,
image_processed_callback=advance)
self.auto_commit_widget.setDisabled(True)
self.progressBarInit()
self.progressBarSet(0.0)
self.setBlocking(True)
f = _executor.submit(run_embedding)
f.add_done_callback(
qconcurrent.methodinvoke(self, "__set_results", (object,)))
task = self._task = namespace(
file_paths_mask=file_paths_mask,
file_paths_valid=file_paths_valid,
file_paths=file_paths,
embedder=embedder,
cancelled=False,
cancel=cancel,
future=f,
)
self._log.debug("Starting embedding task for %i images",
file_paths.size)
return
def commit(self, force=False):
self.Error.clear()
# Kill any running jobs
self.cancel()
assert self.__state == self.State.Pending
if self.data is None:
return
# We commit if auto_commit is on or when we force commit
if not self.auto_commit and not force:
return
# Make sure the dataset is ok
if np.any(np.isnan(self.data.X)):
self.Error.data_has_nans()
return
if len(self.data.domain.attributes) < 1:
self.Error.empty_dataset()
return
# Prepare the tasks to run
queue = TaskQueue(parent=self)
if self.pca_projection is None and self.apply_pca:
queue.push(namespace(task=self._compute_pca_projection))
if self.graph is None:
queue.push(
namespace(task=self._compute_graph, progress_callback=True))
if self.partition is None:
queue.push(namespace(task=self._compute_partition))
# Prepare callbacks
queue.on_progress.connect(lambda val: self.progressBarSet(100 * val))
queue.on_complete.connect(self._processing_complete)
queue.on_complete.connect(self._send_data)
queue.on_exception.connect(self._handle_exceptions)
# Run the task queue
self.progressBarInit()
self.setBlocking(True)
self.__future = self.__executor.submit(queue.start)
self.__state = self.State.Running
def _new_plotdata(self):
self.plotdata = namespace(valid_mask=None,
embedding_coords=None,
axisitems=[],
axes=[],
variables=[],
data=None,
hidecircle=None)
def _new_plotdata(self):
self.plotdata = namespace(
valid_mask=None,
embedding_coords=None,
axisitems=[],
axes=[],
variables=[],
data=None,
hidecircle=None
)
def _new_plotdata(self):
self.plotdata = namespace(
valid_mask=None,
embedding_coords=None,
points=None,
arcarrows=[],
point_labels=[],
rand=None,
data=None,
)
def _new_plotdata(self):
self.plotdata = namespace(
valid_mask=None,
embedding_coords=None,
points=None,
arcarrows=[],
point_labels=[],
rand=None,
data=None,
)
def commit(self):
self.Error.clear()
# Kill any running jobs
self.cancel()
if self.data is None:
return
# Make sure the dataset is ok
if len(self.data.domain.attributes) < 1:
self.Error.empty_dataset()
return
# Preprocess the dataset
if self.preprocessed_data is None:
louvain = Louvain()
self.preprocessed_data = louvain.preprocess(self.data)
# Prepare the tasks to run
queue = TaskQueue(parent=self)
if self.pca_projection is None and self.apply_pca:
queue.push(namespace(task=self._compute_pca_projection))
if self.graph is None:
queue.push(
namespace(task=self._compute_graph, progress_callback=True))
if self.partition is None:
queue.push(namespace(task=self._compute_partition))
# Prepare callbacks
queue.on_progress.connect(lambda val: self.progressBarSet(100 * val))
queue.on_complete.connect(self._on_complete)
queue.on_exception.connect(self._handle_exceptions)
self.__queue = queue
# Run the task queue
self.progressBarInit()
self.setBlocking(True)
self.__future = self.__executor.submit(queue.start)
def __init__(self, pair1, pair2, log_level='DEBUG', *args, **kwargs):
self.files = namespace()
self.files.raw_pair = Fastq(pair1), Fastq(pair2)
self.run = self.files.raw_pair[0].dir.dirname
self.name = self.files.raw_pair[0].sample_name
self.taxon = 'UNKNOWN'
self._logger = self.configure_logging(level=log_level)
self.log("Creating Isolate Instance", lvl="INFO")
self.build_filesystem()
def setScores(self, scores, labels, values, colors, rownames=None):
"""
Set the silhouette scores/labels to for display.
Arguments
---------
scores : (N,) ndarray
The silhouette scores.
labels : (N,) ndarray
A ndarray (dtype=int) of label/clusters indices.
values : list of str
A list of label/cluster names.
colors : (N, 3) ndarray
A ndarray of RGB values.
rownames : list of str, optional
A list (len == N) of row names.
"""
scores = np.asarray(scores, dtype=float)
labels = np.asarray(labels, dtype=int)
if rownames is not None:
rownames = np.asarray(rownames, dtype=object)
if not scores.ndim == labels.ndim == 1:
raise ValueError("scores and labels must be 1 dimensional")
if scores.shape != labels.shape:
raise ValueError("scores and labels must have the same shape")
if rownames is not None and rownames.shape != scores.shape:
raise ValueError("rownames must have the same size as scores")
Ck = np.unique(labels)
if not Ck[0] >= 0 and Ck[-1] < len(values):
raise ValueError(
"All indices in `labels` must be in `range(len(values))`")
cluster_indices = [
np.flatnonzero(labels == i) for i in range(len(values))
]
cluster_indices = [
indices[np.argsort(scores[indices])[::-1]]
for indices in cluster_indices
]
groups = [
namespace(
scores=scores[indices],
indices=indices,
label=label,
rownames=(rownames[indices] if rownames is not None else None),
color=color)
for indices, label, color in zip(cluster_indices, values, colors)
]
self.clear()
self.__groups = groups
self.__setup()
def _preprocess(self, frame):
image_height, image_width = frame.shape[:2]
scale = min(self.h / image_height, self.w / image_width)
processed_image = cv2.resize(frame, None, fx=scale, fy=scale)
processed_image = processed_image.astype('float32').transpose(2, 0, 1)
height, width = processed_image.shape[1], processed_image.shape[2]
im_info = np.array([height, width, 1.0],
dtype='float32') if self.segmentoly_type else None
meta = namespace(
original_size=frame.shape[:2],
processed_size=processed_image.shape[1:3],
)
return processed_image, im_info, meta
def __plot_group(self, X, data, index=None):
p = QPen(self.__get_line_color(None, index), LinePlotStyle.MEAN_WIDTH)
p.setCosmetic(True)
mean = np.nanmean(data.X, axis=0)
mean_curve = self.get_mean_curve(X, mean, p)
range_curve = self.get_range_curve(X, data, p)
error_bar = self.get_error_bar(X, data, mean)
self.graph.addItem(mean_curve)
self.graph.addItem(range_curve)
self.graph.addItem(error_bar)
self.__groups.append(namespace(mean=mean_curve,
range=range_curve,
error_bar=error_bar))
def parse_header(data, pos=0):
(magic,), pos = parse_format('<i', data, pos)
if magic != 0x7eb2fdd6:
raise ValueError("Bad OpenFst TRIE: wrong magic number")
(fst_type,), pos = parse_string(data, pos)
(arc_type,), pos = parse_string(data, pos)
(version, flags, properties, start_state, num_states, num_arcs), pos = parse_format('<iiQqqq', data, pos)
if fst_type != b'const' or arc_type != b'standard' or version != 1:
raise ValueError("Cannot parse OpenFst TRIE: this version of format is not supported")
return namespace(
magic=magic, fst_type=fst_type, arc_type=arc_type, version=version,
flags=flags, properties=properties,
start_state=start_state, num_states=num_states, num_arcs=num_arcs,
), pos
def __plot_mean_with_error(self, X, data, index=None):
pen = QPen(self.__get_line_color(None, index), 4)
pen.setCosmetic(True)
mean = np.nanmean(data.X, axis=0)
mean_curve = pg.PlotDataItem(x=X, y=mean, pen=pen, symbol="o",
symbolSize=5, antialias=True)
self.graph.addItem(mean_curve)
q1, q2, q3 = np.nanpercentile(data.X, [25, 50, 75], axis=0)
bottom = np.clip(mean - q1, 0, mean - q1)
top = np.clip(q3 - mean, 0, q3 - mean)
error_bar = pg.ErrorBarItem(x=X, y=mean, bottom=bottom,
top=top, beam=0.01)
self.graph.addItem(error_bar)
self.__groups.append(namespace(mean=mean_curve, error_bar=error_bar))
def run(self):
imgmeta = []
filescanner = scan(self.startdir)
patterns = ["*.{}".format(fmt.lower()) for fmt in self.formats]
def fnmatch_any(fname, patterns):
return any(
fnmatch.fnmatch(fname.lower(), pattern)
for pattern in patterns)
batch = []
for path in filescanner:
if fnmatch_any(path, patterns):
imeta = image_meta_data(path)
imgmeta.append(imeta)
batch.append(imgmeta)
if self.cancelled:
return
# raise UserInterruptError
if len(batch) == 10 and self.report_progress is not None:
self.report_progress(
namespace(count=len(imgmeta),
lastpath=imgmeta[-1].path,
batch=batch))
batch = []
if batch and self.report_progress is not None:
self.report_progress(
namespace(count=len(imgmeta),
lastpath=imgmeta[-1].path,
batch=batch))
return imgmeta
def _new_plotdata(self):
self.plotdata = namespace(
validmask=None,
embedding_coords=None,
anchors=[],
anchoritem=[],
X=None,
Y=None,
indicators=[],
hidecircle=None,
data=None,
items=[],
topattrs=None,
rand=None,
selection=None, # np.array
)
def _new_plotdata(self):
self.plotdata = namespace(
validmask=None,
embedding_coords=None,
anchors=[],
anchoritem=[],
X=None,
Y=None,
indicators=[],
hidecircle=None,
data=None,
items=[],
topattrs=None,
rand=None,
selection=None, # np.array
)
def setScores(self, scores, labels, values, colors, rownames=None):
"""
Set the silhouette scores/labels to for display.
Arguments
---------
scores : (N,) ndarray
The silhouette scores.
labels : (N,) ndarray
A ndarray (dtype=int) of label/clusters indices.
values : list of str
A list of label/cluster names.
colors : (N, 3) ndarray
A ndarray of RGB values.
rownames : list of str, optional
A list (len == N) of row names.
"""
scores = np.asarray(scores, dtype=float)
labels = np.asarray(labels, dtype=int)
if rownames is not None:
rownames = np.asarray(rownames, dtype=object)
if not scores.ndim == labels.ndim == 1:
raise ValueError("scores and labels must be 1 dimensional")
if scores.shape != labels.shape:
raise ValueError("scores and labels must have the same shape")
if rownames is not None and rownames.shape != scores.shape:
raise ValueError("rownames must have the same size as scores")
Ck = np.unique(labels)
if not Ck[0] >= 0 and Ck[-1] < len(values):
raise ValueError(
"All indices in `labels` must be in `range(len(values))`")
cluster_indices = [np.flatnonzero(labels == i)
for i in range(len(values))]
cluster_indices = [indices[np.argsort(scores[indices])[::-1]]
for indices in cluster_indices]
groups = [
namespace(scores=scores[indices], indices=indices, label=label,
rownames=(rownames[indices] if rownames is not None
else None),
color=color)
for indices, label, color in zip(cluster_indices, values, colors)
]
self.clear()
self.__groups = groups
self.__setup()
def parse_openfst(data, pos=0, base_offset=0):
header, pos = parse_header(data, pos)
pos = align_pos(pos, align=16, base_offset=base_offset)
states = []
for state_idx in range(header.num_states): # pylint: disable=unused-variable
state, pos = parse_state(data, pos)
states.append(state)
pos = align_pos(pos, align=16, base_offset=base_offset)
arcs = []
for arc_idx in range(header.num_arcs): # pylint: disable=unused-variable
arc, pos = parse_arc(data, pos)
arcs.append(arc)
fst = namespace(meta=header, states=states, arcs=arcs)
return fst, pos
def mock_service():
s = namespace(
list=namespace(
organism=namespace(get=lambda: list_organism),
pathway=lambda org:
{"hsa": namespace(get=lambda: list_pathway_hsa)}[org],
),
info=lambda db: {"pathway": namespace(get=lambda: info_pathway)}[db],
get=lambda key:
{"genome:T01001": namespace(get=lambda: genome_T01001)}[key],
)
return s
def read_py_config(filename):
filename = osp.abspath(osp.expanduser(filename))
check_file_exist(filename)
assert filename.endswith('.py')
module_name = osp.basename(filename)[:-3]
if '.' in module_name:
raise ValueError('Dots are not allowed in config file path.')
config_dir = osp.dirname(filename)
sys.path.insert(0, config_dir)
mod = import_module(module_name)
sys.path.pop(0)
return namespace(
**{
name: value
for name, value in mod.__dict__.items()
if not name.startswith('__')
})
def preprocess_inputs(self):
_, _, height, width = self.encoder.input("imgs").shape
target_shape = (height, width)
if os.path.isdir(self.args.input):
inputs = sorted(
os.path.join(self.args.input, inp)
for inp in os.listdir(self.args.input))
else:
inputs = [self.args.input]
for filenm in tqdm(inputs):
image_raw = cv.imread(filenm)
assert image_raw is not None, "Error reading image {}".format(
filenm)
image = preprocess_image(
PREPROCESSING[self.args.preprocessing_type], image_raw,
target_shape)
record = namespace(img_name=filenm, img=image)
self.images_list.append(record)
def mousePressEvent(self, event):
# Reimplemented
if event.button() == Qt.LeftButton:
if event.modifiers() & Qt.ControlModifier:
saction = SelectAction.Toogle
elif event.modifiers() & Qt.AltModifier:
saction = SelectAction.Deselect
elif event.modifiers() & Qt.ShiftModifier:
saction = SelectAction.Select
else:
saction = SelectAction.Clear | SelectAction.Select
self.__selstate = namespace(
modifiers=event.modifiers(), selection=self.__selection, action=saction, rect=None
)
if saction & SelectAction.Clear:
self.__selstate.selection = numpy.array([], dtype=int)
self.setSelection(self.__selstate.selection)
event.accept()
def test_lines_to_edges(self):
"""Show lines_to_edges() works as expected."""
self.challenge.lines = ['1->2', '2->3', '3->4']
expect = [
namespace(head=2, tail=1),
namespace(head=3, tail=2),
namespace(head=4, tail=3)
]
self.assertEqual(expect, self.challenge.lines_to_edges())
expect = [namespace(head=3, tail=2)]
self.assertEqual(expect, self.challenge.lines_to_edges(1, 2))
self.challenge.lines = ['1->2:22']
expect = [namespace(head=2, tail=1, weight=22)]
self.assertEqual(expect, self.challenge.lines_to_edges())
self.challenge.lines = ['1->2, 3', '2->3']
expect = [
namespace(head='2', tail=1),
namespace(head='3', tail=1),
namespace(head=3, tail=2)
]
self.assertEqual(expect, self.challenge.lines_to_edges())
def info(prefix, filename):
if (prefix, filename) in allinforemote:
info = allinforemote[prefix, filename]
else:
info = allinfolocal[prefix, filename]
islocal = (prefix, filename) in allinfolocal
return namespace(prefix=prefix,
filename=filename,
title=info.get("title", filename),
datetime=info.get("datetime", None),
description=info.get("description", None),
reference=info.get("reference", None),
instances=info.get("instances", None),
variables=info.get("variables", None),
target=info.get("target", None),
missing=info.get("missing", None),
tags=info.get("tags", []),
size=info.get("size", None),
islocal=islocal)
def mock_service():
s = namespace(
list=namespace(
organism=namespace(get=lambda: list_organism),
pathway=lambda org: {
"hsa": namespace(get=lambda: list_pathway_hsa)
}[org],
),
info=lambda db:
{"pathway": namespace(get=lambda: info_pathway)}[db],
get=lambda key: {
"genome:T01001": namespace(get=lambda: genome_T01001)
}[key],
)
return s
def mousePressEvent(self, event):
# Reimplemented
if event.button() == Qt.LeftButton:
if event.modifiers() & Qt.ControlModifier:
saction = SelectAction.Toogle
elif event.modifiers() & Qt.AltModifier:
saction = SelectAction.Deselect
elif event.modifiers() & Qt.ShiftModifier:
saction = SelectAction.Select
else:
saction = SelectAction.Clear | SelectAction.Select
self.__selstate = namespace(
modifiers=event.modifiers(),
selection=self.__selection,
action=saction,
rect=None,
)
if saction & SelectAction.Clear:
self.__selstate.selection = np.array([], dtype=int)
self.setSelection(self.__selstate.selection)
event.accept()
def get_pairs(
cls,
path=os.getcwd(),
r1="_R1_",
r2="_R2_",
):
"""Return list of Fastq objects of paired-end reads in directory: `path`"""
if isinstance(path, Dir):
directory = path
elif isinstance(path, str):
directory = Dir(path)
else:
raise TypeError(
f"path must be of type str or Dir. NOT: {type(path)}")
read1 = [
Fastq(file.path)
for file in directory.files(endswith=cls.extensions, contains=r1)
]
return [
namespace(pair1=pair1, pair2=Fastq(pair1.path.replace(r1, r2)))
for pair1 in read1 if os.path.exists(pair1.path.replace(r1, r2))
]
def _setup(self):
"""
Setup the plot.
"""
X = self.data.X
Y = self.data.Y
mask = numpy.bitwise_or.reduce(numpy.isnan(X), axis=1)
mask |= numpy.isnan(Y)
valid = ~mask
X = X[valid, :]
Y = Y[valid]
if self.data.domain.class_var.is_discrete:
Y = Y.astype(int)
X = (X - numpy.mean(X, axis=0))
span = numpy.ptp(X, axis=0)
X[:, span > 0] /= span[span > 0].reshape(1, -1)
if self.initialization == OWFreeViz.Circular:
anchors = linproj.linproj.defaultaxes(X.shape[1]).T
else:
anchors = numpy.random.random((X.shape[1], 2)) * 2 - 1
EX = numpy.dot(X, anchors)
radius = numpy.max(numpy.linalg.norm(EX, axis=1))
jittervec = numpy.random.RandomState(4).rand(*EX.shape) * 2 - 1
jittervec *= 0.01
_, jitterfactor = self.JitterAmount[self.jitter]
colorvar = self._color_var()
shapevar = self._shape_var()
sizevar = self._size_var()
labelvar = self._label_var()
if colorvar is not None:
colors = plotutils.color_data(self.data, colorvar)[valid]
else:
colors = numpy.array([[192, 192, 192]])
colors = numpy.tile(colors, (X.shape[0], 1))
pendata = plotutils.pen_data(colors * 0.8)
colors = numpy.hstack(
[colors, numpy.full((colors.shape[0], 1), float(self.opacity))])
brushdata = plotutils.brush_data(colors)
shapedata = plotutils.shape_data(self.data, shapevar)[valid]
sizedata = size_data(
self.data, sizevar, pointsize=self.point_size)[valid]
if labelvar is not None:
labeldata = plotutils.column_data(self.data, labelvar, valid)
labeldata = [labelvar.str_val(val) for val in labeldata]
else:
labeldata = None
coords = (EX / radius) + jittervec * jitterfactor
item = linproj.ScatterPlotItem(
x=coords[:, 0],
y=coords[:, 1],
brush=brushdata,
pen=pendata,
symbols=shapedata,
size=sizedata,
data=numpy.flatnonzero(valid),
antialias=True,
)
self.plot.addItem(item)
self.plot.setRange(QtCore.QRectF(-1.05, -1.05, 2.1, 2.1))
# minimum visible anchor radius
minradius = self.min_anchor_radius / 100 + 1e-5
axisitems = []
for anchor, var in zip(anchors, self.data.domain.attributes):
axitem = AxisItem(
line=QtCore.QLineF(0, 0, *anchor), label=var.name,)
axitem.setVisible(numpy.linalg.norm(anchor) > minradius)
axitem.setPen(pg.mkPen((100, 100, 100)))
axitem.setArrowVisible(False)
self.plot.addItem(axitem)
axisitems.append(axitem)
hidecircle = QtGui.QGraphicsEllipseItem()
hidecircle.setRect(
QtCore.QRectF(-minradius, -minradius,
2 * minradius, 2 * minradius))
_pen = QtGui.QPen(Qt.lightGray, 1)
_pen.setCosmetic(True)
hidecircle.setPen(_pen)
self.plot.addItem(hidecircle)
self.plotdata = namespace(
validmask=valid,
embedding_coords=EX,
jittervec=jittervec,
anchors=anchors,
mainitem=item,
axisitems=axisitems,
hidecircle=hidecircle,
basecolors=colors,
brushdata=brushdata,
pendata=pendata,
shapedata=shapedata,
sizedata=sizedata,
labeldata=labeldata,
labelitems=[],
densityimage=None,
X=X,
Y=Y,
selectionmask=numpy.zeros_like(valid, dtype=bool)
)
self._update_legend()
self._update_labels()
self._update_density()
def updated(self, **kwargs):
ns = self.__dict__.copy()
ns.update(**kwargs)
return namespace(**ns)
def commit(self):
if self._task is not None:
self.cancel()
if self._image_embedder is None:
self._set_server_info(connected=False)
return
if not self._image_attributes or self._input_data is None:
self.Outputs.embeddings.send(None)
self.Outputs.skipped_images.send(None)
return
self._set_server_info(connected=True)
self.cancel_button.setDisabled(False)
self.cb_image_attr.setDisabled(True)
self.cb_embedder.setDisabled(True)
file_paths_attr = self._image_attributes[self.cb_image_attr_current_id]
file_paths = self._input_data[:, file_paths_attr].metas.flatten()
origin = file_paths_attr.attributes.get("origin", "")
if urlparse(origin).scheme in ("http", "https", "ftp", "data") and \
origin[-1] != "/":
origin += "/"
assert file_paths_attr.is_string
assert file_paths.dtype == np.dtype('O')
file_paths_mask = file_paths == file_paths_attr.Unknown
file_paths_valid = file_paths[~file_paths_mask]
for i, a in enumerate(file_paths_valid):
urlparts = urlparse(a)
if urlparts.scheme not in ("http", "https", "ftp", "data"):
if urlparse(origin).scheme in ("http", "https", "ftp", "data"):
file_paths_valid[i] = urljoin(origin, a)
else:
file_paths_valid[i] = os.path.join(origin, a)
ticks = iter(np.linspace(0.0, 100.0, file_paths_valid.size))
set_progress = qconcurrent.methodinvoke(
self, "__progress_set", (float,))
def advance(success=True):
if success:
set_progress(next(ticks))
def cancel():
task.future.cancel()
task.cancelled = True
task.embedder.set_canceled(True)
embedder = self._image_embedder
def run_embedding(paths):
return embedder(
file_paths=paths, image_processed_callback=advance)
self.auto_commit_widget.setDisabled(True)
self.progressBarInit(processEvents=None)
self.progressBarSet(0.0, processEvents=None)
self.setBlocking(True)
f = self._executor.submit(run_embedding, file_paths_valid)
f.add_done_callback(
qconcurrent.methodinvoke(self, "__set_results", (object,)))
task = self._task = namespace(
file_paths_mask=file_paths_mask,
file_paths_valid=file_paths_valid,
file_paths=file_paths,
embedder=embedder,
cancelled=False,
cancel=cancel,
future=f,
)
self._log.debug("Starting embedding task for %i images",
file_paths.size)
return
#!/usr/bin/env python3
'''
keysym module;
'''
from types import SimpleNamespace as namespace
import curses
## keyname to keycode mapping;
##
## keynames are used in config files;
keyname = namespace()
keyname.space = ord(' ')
keyname.enter = ord('\n')
keyname.left = curses.KEY_LEFT
keyname.right = curses.KEY_RIGHT
keyname.down = curses.KEY_DOWN
keyname.up = curses.KEY_UP
keyname.f1 = curses.KEY_F1
keyname.f2 = curses.KEY_F2
keyname.f3 = curses.KEY_F3
keyname.f4 = curses.KEY_F4
keyname.f5 = curses.KEY_F5
keyname.f6 = curses.KEY_F6
keyname.f7 = curses.KEY_F7
keyname.f8 = curses.KEY_F8
## keysym to keycode mapping;
##
#!/usr/bin/env python3
'''
config module;
'''
from os.path import expanduser
from types import SimpleNamespace as namespace
import yaml
from ncmpy.keysym import keysym as ks
from ncmpy.keysym import name2code as n2c
## config;
conf = namespace()
## default config values;
conf.mpd_host = 'localhost'
conf.mpd_port = 6600
conf.rate_song = True
conf.lyrics_dir = expanduser('~/.ncmpy/lyrics')
## read config files;
for fname in [
expanduser('~/.config/ncmpy/ncmpy.yaml'),
'/etc/ncmpy/ncmpy.yaml',
]:
try:
with open(fname, 'rt') as fp:
data = yaml.load(fp)
except:
def _setup_plot(self):
"""Setup the plot with new curve data."""
assert self.data is not None
data, domain = self.data, self.data.domain
if is_discrete(domain.class_var):
class_col_data, _ = data.get_column_view(domain.class_var)
group_indices = [np.flatnonzero(class_col_data == i)
for i in range(len(domain.class_var.values))]
else:
group_indices = [np.arange(len(data))]
X = np.arange(1, len(domain.attributes)+1)
groups = []
for i, indices in enumerate(group_indices):
if self.classes:
color = self.class_colors[i]
else:
color = QColor(Qt.darkGray)
group_data = data[indices, :]
plot_x, plot_y, connect = disconnected_curve_data(group_data.X, x=X)
color.setAlpha(200)
lightcolor = QColor(color.lighter(factor=150))
lightcolor.setAlpha(150)
pen = QPen(color, 2)
pen.setCosmetic(True)
lightpen = QPen(lightcolor, 1)
lightpen.setCosmetic(True)
hoverpen = QPen(pen)
hoverpen.setWidth(2)
curve = pg.PlotCurveItem(
x=plot_x, y=plot_y, connect=connect,
pen=lightpen, symbolSize=2, antialias=True,
)
self.graph.addItem(curve)
hovercurves = []
for index, profile in zip(indices, group_data.X):
hcurve = HoverCurve(x=X, y=profile, pen=hoverpen,
antialias=True)
hcurve.setToolTip('{}'.format(index))
hcurve._data_index = index
hovercurves.append(hcurve)
self.graph.addItem(hcurve)
mean = np.nanmean(group_data.X, axis=0)
meancurve = pg.PlotDataItem(
x=X, y=mean, pen=pen, size=5, symbol="o", pxMode=True,
symbolSize=5, antialias=True
)
hoverpen = QPen(hoverpen)
hoverpen.setWidth(5)
hc = HoverCurve(x=X, y=mean, pen=hoverpen, antialias=True)
hc.setFlag(QGraphicsItem.ItemIsSelectable, False)
self.graph.addItem(hc)
self.graph.addItem(meancurve)
self.legend_items.append(meancurve)
q1, q2, q3 = np.nanpercentile(group_data.X, [25, 50, 75], axis=0)
# TODO: implement and use a box plot item
errorbar = pg.ErrorBarItem(
x=X, y=mean,
bottom=np.clip(mean - q1, 0, mean - q1),
top=np.clip(q3 - mean, 0, q3 - mean),
beam=0.5
)
self.graph.addItem(errorbar)
groups.append(
namespace(
data=group_data, indices=indices, profiles=curve,
hovercurves=hovercurves, mean=meancurve, boxplot=errorbar)
)
self.__groups = groups
self.__update_visibility()
self.__update_tooltips()
def __init__(self):
super().__init__()
#: widget's runtime state
self.__state = State.NoState
self._imageMeta = []
self._imageCategories = {}
self.__invalidated = False
self.__pendingTask = None
vbox = gui.vBox(self.controlArea)
hbox = gui.hBox(vbox)
self.recent_cb = QComboBox(
sizeAdjustPolicy=QComboBox.AdjustToMinimumContentsLengthWithIcon,
minimumContentsLength=16,
)
self.recent_cb.activated[int].connect(self.__onRecentActivated)
icons = standard_icons(self)
browseaction = QAction(
"Open/Load Images", self,
iconText="\N{HORIZONTAL ELLIPSIS}",
icon=icons.dir_open_icon,
toolTip="Select a directory from which to load the images"
)
browseaction.triggered.connect(self.__runOpenDialog)
reloadaction = QAction(
"Reload", self,
icon=icons.reload_icon,
toolTip="Reload current image set"
)
reloadaction.triggered.connect(self.reload)
self.__actions = namespace(
browse=browseaction,
reload=reloadaction,
)
browsebutton = QPushButton(
browseaction.iconText(),
icon=browseaction.icon(),
toolTip=browseaction.toolTip(),
clicked=browseaction.trigger
)
reloadbutton = QPushButton(
reloadaction.iconText(),
icon=reloadaction.icon(),
clicked=reloadaction.trigger,
default=True,
)
hbox.layout().addWidget(self.recent_cb)
hbox.layout().addWidget(browsebutton)
hbox.layout().addWidget(reloadbutton)
self.addActions([browseaction, reloadaction])
reloadaction.changed.connect(
lambda: reloadbutton.setEnabled(reloadaction.isEnabled())
)
box = gui.vBox(vbox, "Info")
self.infostack = QStackedWidget()
self.info_area = QLabel(
text="No image set selected",
wordWrap=True
)
self.progress_widget = QProgressBar(
minimum=0, maximum=0
)
self.cancel_button = QPushButton(
"Cancel", icon=icons.cancel_icon,
)
self.cancel_button.clicked.connect(self.cancel)
w = QWidget()
vlayout = QVBoxLayout()
vlayout.setContentsMargins(0, 0, 0, 0)
hlayout = QHBoxLayout()
hlayout.setContentsMargins(0, 0, 0, 0)
hlayout.addWidget(self.progress_widget)
hlayout.addWidget(self.cancel_button)
vlayout.addLayout(hlayout)
self.pathlabel = TextLabel()
self.pathlabel.setTextElideMode(Qt.ElideMiddle)
self.pathlabel.setAttribute(Qt.WA_MacSmallSize)
vlayout.addWidget(self.pathlabel)
w.setLayout(vlayout)
self.infostack.addWidget(self.info_area)
self.infostack.addWidget(w)
box.layout().addWidget(self.infostack)
self.__initRecentItemsModel()
self.__invalidated = True
self.__executor = ThreadExecutor(self)
QApplication.postEvent(self, QEvent(RuntimeEvent.Init))
def update_scores(self):
"""Compute the scores and update the histogram.
"""
self.__cancel_pending()
self.clear_plot()
self.scores = None
self.nulldist = None
self.error(0)
grp, split_selection = self.selected_split()
if not self.data or grp is None:
return
_, side, test_type, score_func = self.Scores[self.score_index]
def compute_scores(X, group_indices):
arrays = [X[ind] for ind in group_indices]
return score_func(*arrays, axis=0)
def permute_indices(group_indices, random_state=None):
assert all(ind.dtype.kind == "i" for ind in group_indices)
assert all(ind.ndim == 1 for ind in group_indices)
if random_state is None:
random_state = np.random
joined = np.hstack(group_indices)
random_state.shuffle(joined)
split_ind = np.cumsum([len(ind) for ind in group_indices])
return np.split(joined, split_ind[:-1])
if isinstance(grp, grouputils.RowGroup):
axis = 0
else:
axis = 1
if test_type == OWFeatureSelection.TwoSampleTest:
G1 = grouputils.group_selection_mask(
self.data, grp, split_selection)
G2 = ~G1
indices = [np.flatnonzero(G1), np.flatnonzero(G2)]
elif test_type == self.VarSampleTest:
indices = [grouputils.group_selection_mask(self.data, grp, [i])
for i in range(len(grp.values))]
indices = [np.flatnonzero(ind) for ind in indices]
else:
assert False
if not all(np.count_nonzero(ind) > 0 for ind in indices):
self.error(0, "Target labels most exclude/include at least one "
"value.")
self.scores = None
self.nulldist = None
self.update_data_info_label()
return
X = self.data.X
if axis == 1:
X = X.T
# TODO: Check that each label has more than one measurement,
# raise warning otherwise.
def compute_scores_with_perm(X, indices, nperm=0, rstate=None,
progress_advance=None):
scores = compute_scores(X, indices, )
if progress_advance is not None:
progress_advance()
null_scores = []
if nperm > 0:
if rstate is None:
rstate = np.random.RandomState(0)
for i in range(nperm):
p_indices = permute_indices(indices, rstate)
assert all(pind.shape == ind.shape
for pind, ind in zip(indices, p_indices))
pscore = compute_scores(X, p_indices)
assert pscore.shape == scores.shape
null_scores.append(pscore)
if progress_advance is not None:
progress_advance()
return scores, null_scores
p_advance = concurrent.methodinvoke(
self, "progressBarAdvance", (float,))
state = namespace(cancelled=False, advance=p_advance)
def progress():
if state.cancelled:
raise concurrent.CancelledError
else:
state.advance(100 / (nperm + 1))
self.progressBarInit()
set_scores = concurrent.methodinvoke(
self, "__set_score_results", (concurrent.Future,))
nperm = self.permutations_count if self.compute_null else 0
self.__scores_state = state
self.__scores_future = self._executor.submit(
compute_scores_with_perm, X, indices, nperm,
progress_advance=progress)
self.__scores_future.add_done_callback(set_scores)
def start(self):
"""
Start/execute the image indexing operation
"""
self.error()
self.__invalidated = False
if self.currentPath is None:
return
if self.__state == State.Processing:
assert self.__pendingTask is not None
log.info("Starting a new task while one is in progress. "
"Cancel the existing task (dir:'{}')"
.format(self.__pendingTask.startdir))
self.cancel()
startdir = self.currentPath
self.__setRuntimeState(State.Processing)
report_progress = methodinvoke(
self, "__onReportProgress", (object,))
task = ImageScan(startdir, report_progress=report_progress)
# collect the task state in one convenient place
self.__pendingTask = taskstate = namespace(
task=task,
startdir=startdir,
future=None,
watcher=None,
cancelled=False,
cancel=None,
)
def cancel():
# Cancel the task and disconnect
if taskstate.future.cancel():
pass
else:
taskstate.task.cancelled = True
taskstate.cancelled = True
try:
taskstate.future.result(timeout=3)
except UserInterruptError:
pass
except TimeoutError:
log.info("The task did not stop in in a timely manner")
taskstate.watcher.finished.disconnect(self.__onRunFinished)
taskstate.cancel = cancel
def run_image_scan_task_interupt():
try:
return task.run()
except UserInterruptError:
# Suppress interrupt errors, so they are not logged
return
taskstate.future = self.__executor.submit(run_image_scan_task_interupt)
taskstate.watcher = FutureWatcher(taskstate.future)
taskstate.watcher.finished.connect(self.__onRunFinished)
def _setup_plot(self):
"""Setup the plot with new curve data."""
assert self.data is not None
self.graph.clear()
data, domain = self.data, self.data.domain
var = domain[self.group_var]
class_col_data, _ = data.get_column_view(var)
group_indices = [np.flatnonzero(class_col_data == i)
for i in range(len(self.classes))]
self.graph.getAxis('bottom').setTicks([
[(i+1, str(a)) for i, a in enumerate(self.graph_variables)]
])
X = np.arange(1, len(self.graph_variables)+1)
groups = []
for i, indices in enumerate(group_indices):
if len(indices) == 0:
groups.append(None)
else:
if self.classes:
color = self.class_colors[i]
else:
color = QColor(Qt.darkGray)
group_data = data[indices, self.graph_variables]
plot_x, plot_y, connect = disconnected_curve_data(group_data.X, x=X)
color.setAlpha(200)
lightcolor = QColor(color.lighter(factor=150))
lightcolor.setAlpha(150)
pen = QPen(color, 2)
pen.setCosmetic(True)
lightpen = QPen(lightcolor, 1)
lightpen.setCosmetic(True)
curve = pg.PlotCurveItem(
x=plot_x, y=plot_y, connect=connect,
pen=lightpen, symbolSize=2, antialias=True,
)
self.graph.addItem(curve)
mean = np.nanmean(group_data.X, axis=0)
meancurve = pg.PlotDataItem(
x=X, y=mean, pen=pen, size=5, symbol="o", pxMode=True,
symbolSize=5, antialias=True
)
self.graph.addItem(meancurve)
q1, q2, q3 = np.nanpercentile(group_data.X, [25, 50, 75], axis=0)
# TODO: implement and use a box plot item
errorbar = pg.ErrorBarItem(
x=X, y=mean,
bottom=np.clip(mean - q1, 0, mean - q1),
top=np.clip(q3 - mean, 0, q3 - mean),
beam=0.5
)
self.graph.addItem(errorbar)
groups.append(
namespace(
data=group_data, indices=indices,
profiles=curve, mean=meancurve,
boxplot=errorbar)
)
self.__groups = groups
self.__update_visibility()
def __init__(self, parent=None):
super().__init__(parent)
self.data = None
self.subset_data = None
self._subset_mask = None
self._selection_mask = None
self._item = None
self.__legend = None
self.__selection_item = None
self.__replot_requested = False
box = gui.widgetBox(self.controlArea, "Axes")
box1 = gui.widgetBox(box, "Displayed", margin=0)
box1.setFlat(True)
self.active_view = view = QListView(
sizePolicy=QSizePolicy(QSizePolicy.Minimum, QSizePolicy.Ignored),
selectionMode=QListView.ExtendedSelection,
dragEnabled=True,
defaultDropAction=Qt.MoveAction,
dragDropOverwriteMode=False,
dragDropMode=QListView.DragDrop,
showDropIndicator=True,
minimumHeight=50,
)
view.viewport().setAcceptDrops(True)
movedown = QAction(
"Move down", view,
shortcut=QKeySequence(Qt.AltModifier | Qt.Key_Down),
triggered=self.__deactivate_selection
)
view.addAction(movedown)
self.varmodel_selected = model = DnDVariableListModel(
parent=self)
model.rowsInserted.connect(self._invalidate_plot)
model.rowsRemoved.connect(self._invalidate_plot)
model.rowsMoved.connect(self._invalidate_plot)
view.setModel(model)
box1.layout().addWidget(view)
box1 = gui.widgetBox(box, "Other", margin=0)
box1.setFlat(True)
self.other_view = view = QListView(
sizePolicy=QSizePolicy(QSizePolicy.Minimum, QSizePolicy.Ignored),
selectionMode=QListView.ExtendedSelection,
dragEnabled=True,
defaultDropAction=Qt.MoveAction,
dragDropOverwriteMode=False,
dragDropMode=QListView.DragDrop,
showDropIndicator=True,
minimumHeight=50
)
view.viewport().setAcceptDrops(True)
moveup = QtGui.QAction(
"Move up", view,
shortcut=QKeySequence(Qt.AltModifier | Qt.Key_Up),
triggered=self.__activate_selection
)
view.addAction(moveup)
self.varmodel_other = model = DnDVariableListModel(parent=self)
view.setModel(model)
box1.layout().addWidget(view)
box = gui.widgetBox(self.controlArea, "Jittering")
gui.comboBox(box, self, "jitter_value",
items=["None", "0.01%", "0.1%", "0.5%", "1%", "2%"],
callback=self._invalidate_plot)
box.setSizePolicy(QSizePolicy.Expanding, QSizePolicy.Fixed)
box = gui.widgetBox(self.controlArea, "Points")
box.setSizePolicy(QSizePolicy.Minimum, QSizePolicy.Maximum)
self.colorvar_model = itemmodels.VariableListModel(parent=self)
self.shapevar_model = itemmodels.VariableListModel(parent=self)
self.sizevar_model = itemmodels.VariableListModel(parent=self)
self.labelvar_model = itemmodels.VariableListModel(parent=self)
form = QtGui.QFormLayout(
formAlignment=Qt.AlignLeft,
labelAlignment=Qt.AlignLeft,
fieldGrowthPolicy=QtGui.QFormLayout.AllNonFixedFieldsGrow,
spacing=8
)
box.layout().addLayout(form)
cb = gui.comboBox(box, self, "color_index",
callback=self._on_color_change)
cb.setModel(self.colorvar_model)
form.addRow("Colors", cb)
alpha_slider = QSlider(
Qt.Horizontal, minimum=10, maximum=255, pageStep=25,
tickPosition=QSlider.TicksBelow, value=self.alpha_value)
alpha_slider.valueChanged.connect(self._set_alpha)
form.addRow("Opacity", alpha_slider)
cb = gui.comboBox(box, self, "shape_index",
callback=self._on_shape_change)
cb.setModel(self.shapevar_model)
form.addRow("Shape", cb)
cb = gui.comboBox(box, self, "size_index",
callback=self._on_size_change)
cb.setModel(self.sizevar_model)
form.addRow("Size", cb)
size_slider = QSlider(
Qt.Horizontal, minimum=3, maximum=30, value=self.point_size,
pageStep=3,
tickPosition=QSlider.TicksBelow)
size_slider.valueChanged.connect(self._set_size)
form.addRow("", size_slider)
toolbox = gui.widgetBox(self.controlArea, "Zoom/Select")
toollayout = QtGui.QHBoxLayout()
toolbox.layout().addLayout(toollayout)
gui.auto_commit(self.controlArea, self, "auto_commit", "Commit")
# Main area plot
self.view = pg.GraphicsView(background="w")
self.view.setRenderHint(QtGui.QPainter.Antialiasing, True)
self.view.setFrameStyle(QtGui.QFrame.StyledPanel)
self.viewbox = pg.ViewBox(enableMouse=True, enableMenu=False)
self.viewbox.grabGesture(Qt.PinchGesture)
self.view.setCentralItem(self.viewbox)
self.mainArea.layout().addWidget(self.view)
self.selection = PlotSelectionTool(
self, selectionMode=PlotSelectionTool.Lasso)
self.selection.setViewBox(self.viewbox)
self.selection.selectionFinished.connect(self._selection_finish)
self.zoomtool = PlotZoomTool(self)
self.pantool = PlotPanTool(self)
self.pinchtool = PlotPinchZoomTool(self)
self.pinchtool.setViewBox(self.viewbox)
self.continuous_palette = colorpalette.ContinuousPaletteGenerator(
QtGui.QColor(220, 220, 220),
QtGui.QColor(0, 0, 0),
False
)
self.discrete_palette = colorpalette.ColorPaletteGenerator(13)
def icon(name):
path = "icons/Dlg_{}.png".format(name)
path = pkg_resources.resource_filename(widget.__name__, path)
return QtGui.QIcon(path)
actions = namespace(
zoomtofit=QAction(
"Zoom to fit", self, icon=icon("zoom_reset"),
shortcut=QKeySequence(Qt.ControlModifier | Qt.Key_0),
triggered=lambda:
self.viewbox.setRange(QRectF(-1.05, -1.05, 2.1, 2.1))),
zoomin=QAction(
"Zoom in", self,
shortcut=QKeySequence(QKeySequence.ZoomIn),
triggered=lambda: self.viewbox.scaleBy((1 / 1.25, 1 / 1.25))),
zoomout=QAction(
"Zoom out", self,
shortcut=QKeySequence(QKeySequence.ZoomOut),
triggered=lambda: self.viewbox.scaleBy((1.25, 1.25))),
select=QAction(
"Select", self, checkable=True, icon=icon("arrow"),
shortcut=QKeySequence(Qt.ControlModifier + Qt.Key_1)),
zoom=QAction(
"Zoom", self, checkable=True, icon=icon("zoom"),
shortcut=QKeySequence(Qt.ControlModifier + Qt.Key_2)),
pan=QAction(
"Pan", self, checkable=True, icon=icon("pan_hand"),
shortcut=QKeySequence(Qt.ControlModifier + Qt.Key_3)),
)
self.addActions([actions.zoomtofit, actions.zoomin, actions.zoomout])
group = QtGui.QActionGroup(self, exclusive=True)
group.addAction(actions.select)
group.addAction(actions.zoom)
group.addAction(actions.pan)
actions.select.setChecked(True)
currenttool = self.selection
self.selection.setViewBox(None)
def activated(action):
nonlocal currenttool
if action is actions.select:
tool, cursor = self.selection, Qt.ArrowCursor
elif action is actions.zoom:
tool, cursor = self.zoomtool, Qt.ArrowCursor
elif action is actions.pan:
tool, cursor = self.pantool, Qt.OpenHandCursor
else:
assert False
currenttool.setViewBox(None)
tool.setViewBox(self.viewbox)
self.viewbox.setCursor(QtGui.QCursor(cursor))
currenttool = tool
group.triggered[QAction].connect(activated)
def button(action):
b = QtGui.QToolButton()
b.setDefaultAction(action)
return b
toollayout.addWidget(button(actions.select))
toollayout.addWidget(button(actions.zoom))
toollayout.addWidget(button(actions.pan))
toollayout.addSpacing(4)
toollayout.addWidget(button(actions.zoomtofit))
toollayout.addStretch()
toolbox.setSizePolicy(QSizePolicy.Expanding, QSizePolicy.Maximum)
