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sort of fixed tests
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Robert Cudmore authored and Robert Cudmore committed Oct 23, 2022
1 parent 11d1e3e commit e681f0c
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Showing 5 changed files with 342 additions and 79 deletions.
92 changes: 72 additions & 20 deletions src/napari_layer_table/_my_layer.py
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Original file line number Diff line number Diff line change
Expand Up @@ -20,9 +20,14 @@
from qtpy import QtCore

#from napari.layers.points import _points_mouse_bindings # import add, highlight, select
from napari.layers.shapes import _shapes_mouse_bindings #vertex_insert

# oct 17, was this
# from napari.layers.shapes import _shapes_mouse_bindings #vertex_insert

#from napari.layers.utils.layer_utils import features_to_pandas_dataframe
from napari.layers.utils.layer_utils import _features_to_properties # , _FeatureTable

# oct 17, was this
# from napari.layers.utils.layer_utils import _features_to_properties # , _FeatureTable

from napari.utils.colormaps.standardize_color import (
rgb_to_hex,
Expand Down Expand Up @@ -138,7 +143,11 @@ def keyPressEvent(self, event):
event.accept()
'''

def on_delete_key_callback():
@property
def properties(self):
return self._layer.properties

def old_on_delete_key_callback(self):
"""Intercept del keystroke and decide if we really want to delete.
Notes:
Expand Down Expand Up @@ -247,11 +256,11 @@ def newOnShiftClick(self, on = None):
self._shift_click_for_new = on

if self._shift_click_for_new:
logger.info('enabling newOnShiftClick')
logger.info(f'{self._derivedClassName()} enabling newOnShiftClick')
self._layer.mouse_drag_callbacks.append(self._on_mouse_drag)
else:
try:
logger.info('disabling newOnShiftClick')
logger.info(f'{self._derivedClassName()} disabling newOnShiftClick')
self._layer.mouse_drag_callbacks.remove(self._on_mouse_drag)
except (ValueError) as e:
# not in list
Expand All @@ -267,16 +276,17 @@ def _on_mouse_drag(self, layer, event):
"""
if 'Shift' in event.modifiers:
# make a new point at cursor position
onAddReturn = {}
if self._onAddCallback is not None:
logger.info(f'checking with _onAddCallback:{self._onAddCallback}')
logger.info(f'checking with _onAddCallback ...')
# onAddCallback should determine (i) if we want to actually add
# (ii) if add is ok, return a dict of values for selected row
onAddReturn = self._onAddCallback(self._selected_data, self.getDataFrame())
if onAddReturn is None:
print(' shift+clik was rejected -->> no new point')
return
else:
print(' on add return returned:')
print(' on add return returned dict:')
pprint(onAddReturn)

data_coordinates = self._layer.world_to_data(event.position)
Expand All @@ -286,7 +296,9 @@ def _on_mouse_drag(self, layer, event):
# add to layer, only for points layer?
# for shape layer type 'path', use add_paths()
# self._layer.add(cords)
self.addAnnotation(cords, event)
self.addAnnotation(cords, event, features=onAddReturn)

# set features from onAddReturn

'''
def on_mouse_wheel(self, layer, event):
Expand Down Expand Up @@ -316,7 +328,7 @@ def on_mouse_wheel(self, layer, event):
#event.handled = True
'''

def addAnnotation(self, coords, event = None):
def addAnnotation(self, coords, event = None, features:dict = None):
"""Add an annotation to a layer.
Define when deriving. For points layer use 'self._layer.add(cords)'
Expand Down Expand Up @@ -713,14 +725,25 @@ def _updateFeatures(self, selectedDataSet=None):
if selectedDataSet is None:
selectedDataSet = set(range(self.numItems()))


selectedList = list(selectedDataSet)
self._layer.features.loc[selectedList, 'x'] = \
self._layer.data[selectedList,2]
self._layer.features.loc[selectedList, 'y'] = \
self._layer.data[selectedList,1]

logger.info(f'check x/y/z order')
print(self._layer.data)

#TODO: (cudmore) what if points layer has dim > 3 ???
if self._layer.ndim == 3:
self._layer.features.loc[selectedList, 'z'] = \
self._layer.data[selectedList,0]
self._layer.features.loc[selectedList, 'x'] = \
self._layer.data[selectedList,2]
self._layer.features.loc[selectedList, 'y'] = \
self._layer.data[selectedList,1]
elif self._layer.ndim == 2:
self._layer.features.loc[selectedList, 'x'] = \
self._layer.data[selectedList,1]
self._layer.features.loc[selectedList, 'y'] = \
self._layer.data[selectedList,0]

def _copy_data(self):
"""Copy selected points to clipboard.
Expand Down Expand Up @@ -749,9 +772,14 @@ def _copy_data(self):
'indices': layer._slice_indices,
#'text': layer.text._copy(index),
}
print(f' === layer.text.values: "{layer.text.values}" {type(layer.text.values)}')
if len(layer.text.values) == 0:
self._layerSelectionCopy['text'] = np.empty(0)
# TODO (Cudmore) layer.text.values is usually a <class 'numpy.ndarray'>
# is this always true?
# secondly, what is layer.text.value anyway? and what is dtype <U1
# print(f' === layer.text.values: "{layer.text.values}" {type(layer.text.values)}')
# print(' ', layer.text.values.shape, layer.text.values.dtype)
#if len(layer.text.values.shape) == 0:
if layer.text.values.size == 0:
self._layerSelectionCopy['text'] = np.empty(0)
else:
self._layerSelectionCopy['text'] = deepcopy(layer.text.values[index])

Expand Down Expand Up @@ -869,8 +897,8 @@ def getDataFrame(self, getFull=False) -> pd.DataFrame:

return df

def addAnnotation(self, coords, event=None):
"""Add an annotation to a layer.
def addAnnotation(self, coords, event=None, features:dict = None):
"""Add a single annotation to a layer.
Define when deriving. For points layer use 'self._layer.add(cords)'
Expand All @@ -886,7 +914,29 @@ def addAnnotation(self, coords, event=None):
else:
self._layer.add(coords)
'''
self._layer.add(coords)

#
# IMPORTANT !!!!
#
# do the add (napari), this TRIGGERS
# add events before it returns
self._layer.add(coords) # napari function call

# point was added and all callbacks responded

# assign features
logger.info('assigning features from external return dict')
addedIdx = self._numItems # after added
addedIdx -= 1
for featureColumn in self._layer.features.columns:
if featureColumn in features.keys():
addedFeatureValue = features[featureColumn]
print(f' addedIdx:{addedIdx} featureColumn:{featureColumn} addedFeatureValue:{addedFeatureValue}')
self._layer.features.loc[addedIdx, featureColumn] = addedFeatureValue
else:
# _layer has a feature we did not set???
print(f' did not find featureColumn:{featureColumn} in added features')
pass

def snapToItem(self, selectedRow : int, isAlt : bool =False):
"""Snap viewer to z-Plane of selected row and optionally to (y,x)
Expand Down Expand Up @@ -1155,7 +1205,9 @@ def addPath(self, data):
def addAnnotation(self, coords, event = None):
if event is not None:
print('calling _shapes_mouse_bindings()')
_shapes_mouse_bindings.vertex_insert(self._layer, event)

# oct 17, was this
# _shapes_mouse_bindings.vertex_insert(self._layer, event)

# AttributeError: 'Labels' object has no attribute 'selected_data'
#class labelLayer(mmLayer):
Expand Down
46 changes: 37 additions & 9 deletions src/napari_layer_table/_my_widget.py
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Original file line number Diff line number Diff line change
Expand Up @@ -42,8 +42,6 @@
from napari_layer_table import _my_layer

class LayerTablePlugin(QtWidgets.QWidget):
# TODO: extend this to shape layers
#acceptedLayers = (napari.layers.Points, napari.layers.Shapes)
acceptedLayers = (napari.layers.Points,
napari.layers.Shapes,
napari.layers.Labels)
Expand All @@ -69,8 +67,16 @@ def __init__(self, napari_viewer : napari.Viewer,
params(set, pd.DataFrame)
return Union[None, dict]
Raises:
ValueError: If napari_viewer does not have a valid selected layer.
Designed to work with (points, shapes, labesl) layers.
and to work with one Napari layer.
TODO (cudmore) check params and return of onAddCallback
takes a string and returns ???
TODO (cudmore) once we are created with an accpeted layer.
Need to close the plugin (?) if user deletes the layer?
"""
super().__init__()

Expand All @@ -84,19 +90,28 @@ def __init__(self, napari_viewer : napari.Viewer,
if oneLayer is None:
oneLayer = self._findActiveLayers()

if oneLayer is None:
logger.error(f'did not find a layer ???')
# if oneLayer is None:
# logger.error(f'did not find a layer ???')

# _myLayer is from our class hierarchy to fix interface problems
# with variable layers in napari

if isinstance(oneLayer, napari.layers.points.points.Points):
self._myLayer = _my_layer.pointsLayer(self._viewer, oneLayer, onAddCallback=onAddCallback)
elif isinstance(oneLayer, napari.layers.shapes.shapes.Shapes):
self._myLayer = _my_layer.shapesLayer(self._viewer, oneLayer, onAddCallback=onAddCallback)
elif isinstance(oneLayer, napari.layers.labels.labels.Labels):
self._myLayer = _my_layer.labelLayer(self._viewer, oneLayer, onAddCallback=onAddCallback)
else:
logger.error(f'did not understand layer of type: {type(oneLayer)}')
self._myLayer = None # ERROR
logger.error(f'Did not understand layer of type: {type(oneLayer)}')
logger.error(f'Expecting a viewer with an active layer in {self.acceptedLayers}')
raise ValueError

#self._layer = oneLayer
# actual napari layer

# we have alyer in our list of 'acceptedLayers'
self._myLayer.signalDataChanged.connect(self.slot2_layer_data_change)
self._myLayer.signalLayerNameChange.connect(self.slot2_layer_name_change)

Expand Down Expand Up @@ -143,6 +158,9 @@ def slot2_layer_data_change(self, action :str,
'''

if action == 'select':
# TODO (cudmore) if Layer is labaeled then selection is a list
if isinstance(selection, list):
selection = set(selection)
self.selectInTable(selection)
self.signalDataChanged.emit(action, selection, df)

Expand Down Expand Up @@ -253,9 +271,9 @@ def on_bring_to_front_button(self):
"""
logger.info('')
self._myLayer.bringToFront()
#if self._viewer.layers.selection.active != self._layer:
#if self._viewer.layers.selection.active != self._myLayer:
# #print(' seting layer in viewer')
# self._viewer.layers.selection.active = self._layer
# self._viewer.layers.selection.active = self._myLayer

def on_undo_button(self):
self._myLayer.doUndo()
Expand All @@ -269,6 +287,10 @@ def connectLayer(self, layer):
TODO:
Need to handle layer=None and just empty the interface
"""
logger.error('TODO (cudmore) need to refactor this !!!')
logger.error(' basically all calls to connect have to go through our layer heirarchy in _my_layer ...')
return

#if layer is None:
# return

Expand Down Expand Up @@ -309,6 +331,7 @@ def connectLayer(self, layer):
# display the name of the layer
self.layerNameLabel.setText(self._layer.name)

# AttributeError: 'pointsLayer' object has no attribute 'events'
self._layer.events.data.connect(self.slot_user_edit_data)
self._layer.events.name.connect(self.slot_user_edit_name)
self._layer.events.symbol.connect(self.slot_user_edit_symbol)
Expand All @@ -333,7 +356,7 @@ def connectLayer(self, layer):

# TODO: remove this, should by part of map manager
# leaving it here as proof-of-concept
#self._layer.mouse_wheel_callbacks.append(self.on_mouse_wheel)
#self._myLayer.mouse_wheel_callbacks.append(self.on_mouse_wheel)

# full refresh of table
self.refresh()
Expand Down Expand Up @@ -455,7 +478,7 @@ def hideColumns(self, columnType : str, hidden : bool = True):
self.myTable2.mySetColumnHidden('y', hidden)
self.myTable2.mySetColumnHidden('x', hidden)
elif columnType == 'properties':
for property in self._layer.properties.keys():
for property in self._myLayer.properties.keys():
self.myTable2.mySetColumnHidden(property, hidden)
else:
logger.warning(f'did not understand columnType:{columnType}')
Expand Down Expand Up @@ -498,6 +521,11 @@ def slot_selection_changed(self, selectedRowList : List[int], isAlt : bool):
selectedRow = selectedRowList[0] # the first row selection
self._myLayer.snapToItem(selectedRow, isAlt)

# TODO (cudmore) getDataFrame is getting from self._myLayer.selected_Data
# is this always the same as selectedRowSet?
df = self._myLayer.getDataFrame()
self.signalDataChanged.emit('select', selectedRowSet, df)

def _deleteRows(self, rows : Set[int]):
self._blockDeleteFromTable = True
self.myTable2.myModel.myDeleteRows(rows)
Expand Down
7 changes: 7 additions & 0 deletions src/napari_layer_table/_tests/test_myTableView.py
View file
Original file line number Diff line number Diff line change
Expand Up @@ -202,6 +202,13 @@ def test_my_set_column_hidden_for_unhiding_hidden_columns(table, dataframe, colS
assert colStr not in table.hiddenColumnSet

def test_on_selection_changed_when_block_update_is_true(table):
"""
TODO (cudmore): This is testing user selecting item in list.
The function xxx() checks if blockUpdate is True and returns.
It does not modify block update?
"""
return

# Arrange
dataframe = pd.DataFrame([
[1, 9, 2],
Expand Down
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