- Added TestPickerModel(default picker model) and TestPickFilModel(fi…

…lament model) for test

- Tested default picking and filament pincking
- Fixed errors from datavis picker model refactoring

emvis/__init__.py

@@ -8,3 +8,4 @@
 from . import utils
 from . import models
 from . import views
+from . import tests

emvis/models/_empicker.py

@@ -188,15 +188,19 @@ def getParams(self):
  [scoreThreshold, useColor]
  ])
 
- def changeParam(self, micId, paramName, paramValue, getValuesFunc):
+ def onParamChanged(self, micId, paramName, paramValues):
  # Most cases here will modify the current coordinates
- r = self.Result(currentCoordsChanged=True, tableModelChanged=True)
+ d = {'micId': micId,
+ 'currentCoordsChanged': True,
+ 'tableModelChanged': True}
+ n = True
 
  if paramName == 'scoreThreshold':
- self._scoreThreshold = getValuesFunc()['scoreThreshold']
+ self._scoreThreshold = paramValues['scoreThreshold']
  elif paramName == 'useColor':
- self._useColor = getValuesFunc()['useColor']
+ self._useColor = paramValues['useColor']
  else:
- r = self.Result() # No modification
+ n = False # No modification
 
- return r
+ if n:
+ self.notifyEvent(type=dv.models.PICK_EVT_DATA_CHANGED, info=d)

emvis/models/_emtable_model.py

@@ -24,7 +24,8 @@ def __init__(self, tableSource, **kwargs):
  * string: This should be the path from where to read
  the table(s). The first table will be loaded by default.
  * tuple (string, string): Here you can specify the path and
- the name of the table that you want to be loaded by default.
+ the name of the table that you want to be loaded by
+ default.
 
  Keyword Arguments:
  imageManager=value Provide an ImageManager that can be used

emvis/tests/__init__.py

@@ -0,0 +1,2 @@
+
+from .test_common import TestPickerModel, TestPickFilModel

emvis/tests/test_common.py

@@ -0,0 +1,208 @@
+
+import os
+from random import randint
+
+import datavis as dv
+import emvis.models as em_models
+
+class TestPickerModel(em_models.EmPickerModel):
+ """ Em picker data model with direct access to ImageManager """
+
+ def __init__(self, inputDir, coordDir, imageManager=None):
+ """
+ Create a new instance of :class:`~TestPickerModel`.
+
+ Args:
+ inputDir: Directory with the resulting picking dir
+ imageManager: optional :class:`~emvis.utils.ImageManager` class to
+ read micrographs from disk.
+ """
+ em_models.EmPickerModel.__init__(self, imageManager=imageManager)
+ self._inputDir = inputDir
+ self._coordDir = coordDir
+ self._scoreThreshold = 0.0
+ self._useColor = False
+
+ self._loadData()
+
+ def _parseEmPickCoordinates(self, path):
+ """ Parse (x, y) coordinates from a text file assuming
+ that the first two columns on each line are x and y.
+ Other specifications can be:
+ - x y label
+ - x1 y1 width height
+ - x1 y1 width height label
+ """
+ with open(path) as f:
+ Coord = dv.models.Coordinate
+ index = 0
+ for line in f:
+ li = line.strip()
+ index += 1
+ t = randint(0, 10) # FIXME[hv] use random threshold
+ if li:
+ parts = li.strip().split()
+ size = len(parts)
+ if size == 2 or size == 4: # (x, y) or (x1,y1,width,height)
+ yield Coord(int(parts[0]), int(parts[1]), "",
+ threshold=t)
+ elif size == 3: # (x, y, label)
+ yield Coord(int(parts[0]), int(parts[1]), str(parts[2]),
+ threshold=t)
+ elif size == 5: # (x1, y1, width, height, label):
+ yield Coord(int(parts[0]), int(parts[1]), str(parts[4]),
+ threshold=t)
+ else:
+ raise Exception(
+ "Unsupported coordinate specification:\n"
+ "path: %s" % path % "line: %d" % index)
+
+ def _initLabels(self):
+ """ Initialize the labels for this PickerModel. """
+ colors = [
+ "#1EFF00",
+ "#DD0014"
+ ]
+ for i, c in enumerate(colors):
+ name = str(i)
+ self._labels[name] = self.Label(name=name, color=c)
+ self._labels['D'] = self._labels['0']
+
+ def _input(self, filename):
+ return os.path.join(self._inputDir, filename)
+
+ def _coord(self, filename):
+ return os.path.join(self._coordDir, filename)
+
+ def _loadData(self):
+ self._loadedMics = set()
+
+ if not os.path.exists(self._inputDir):
+ raise Exception("Expecting directory '%s'" % self._inputDir)
+
+ if not os.path.exists(self._coordDir):
+ raise Exception("Expecting directory '%s'" % self._coordDir)
+
+ micId = 0
+ for micName in os.listdir(self._inputDir):
+ micId += 1
+ mic = dv.models.Micrograph(micId=micId, path=self._input(micName))
+ self.addMicrograph(mic)
+ self.beginReadCoordinates(micId)
+
+ def readCoordinates(self, micId):
+ if not micId in self._loadedMics:
+ self._loadedMics.add(micId)
+ mic = self.getMicrograph(micId)
+ micName = os.path.split(mic.getPath())[-1]
+ coordPath = self._coord(os.path.splitext(micName)[0] + '.box')
+
+ if os.path.exists(coordPath):
+ return self._parseEmPickCoordinates(coordPath)
+ return []
+
+ def createCoordinate(self, x, y, label, **kwargs):
+ """
+ Return a Coordinate object. This is the preferred way to create
+ Coordinates objects, ensuring that the object contains all
+ the additional properties related to the model.
+ Subclasses should implement this method
+ """
+ return dv.models.Coordinate(x, y, 'M', threshold=1, **kwargs)
+
+ def iterCoordinates(self, micId):
+ # Re-implement this to show only these above the threshold
+ # or with a different color (label)
+ for coord in self._getCoordsList(micId):
+ good = coord.threshold > self._scoreThreshold
+ coord.label = '0' if good else '1'
+ if good or self._useColor:
+ yield coord
+
+ def getColumns(self):
+ """ Return a Column list that will be used to display micrographs. """
+ return [
+ dv.models.ColumnConfig('Micrograph', dataType=dv.models.TYPE_STRING,
+ editable=False),
+ dv.models.ColumnConfig('Coordinates', dataType=dv.models.TYPE_INT,
+ editable=False),
+ dv.models.ColumnConfig('Id', dataType=dv.models.TYPE_INT,
+ editable=False, visible=False),
+ ]
+
+ def getValue(self, row, col):
+ """ Return the value in this (row, column) from the micrographs table.
+ """
+ mic = self.getMicrographByIndex(row)
+
+ if col == 0: # Name
+ return os.path.basename(mic.getPath())
+ elif col == 1: # Coordinates
+ # Use real coordinates number for already loaded micrographs
+ return len(mic)
+ elif col == 2: # Id
+ return mic.getId()
+ else:
+ raise Exception("Invalid column value '%s'" % col)
+
+ def getParams(self):
+ Param = dv.models.Param
+ scoreThreshold = Param('scoreThreshold', 'int', value=5,
+ display='slider', range=(0, 10),
+ label='Score threshold',
+ help='Display coordinates with score above '
+ 'this value.')
+
+ useColor = Param('useColor', 'bool', value=self._useColor,
+ label='Color coordinates \nwith score above?')
+
+ return dv.models.Form([
+ [scoreThreshold, useColor]
+ ])
+
+ def onParamChanged(self, micId, paramName, paramValues):
+ # Most cases here will modify the current coordinates
+ d = {'micId': micId,
+ 'currentCoordsChanged': True,
+ 'tableModelChanged': True}
+ n = True
+
+ if paramName == 'scoreThreshold':
+ self._scoreThreshold = paramValues['scoreThreshold']
+ elif paramName == 'useColor':
+ self._useColor = paramValues['useColor']
+ else:
+ n = False # No modification
+
+ if n:
+ self.notifyEvent(type=dv.models.PICK_EVT_DATA_CHANGED, info=d)
+
+
+class TestPickFilModel(TestPickerModel):
+
+ def _parseEmPickCoordinates(self, path):
+ """ Parse (x1, y1, x2, y2) coordinates from a text file assuming
+ that the first four columns on each line are x1, y1, x2, y2.
+ Other specifications can be:
+ - x1 y1 x2 y2 label
+ """
+ with open(path) as f:
+ Coord = dv.models.Coordinate
+ index = 0
+ for line in f:
+ li = line.strip()
+ index += 1
+ t = randint(0, 10) # FIXME[hv] use random threshold
+ if li:
+ parts = li.strip().split()
+ size = len(parts)
+ if size == 4: # (x1, y1, x2, y2)
+ yield Coord(int(parts[0]), int(parts[1]), "",
+ threshold=t, x2=parts[2], y2=parts[3])
+ elif size == 5: # (x1, y1, x2, y2, label):
+ yield Coord(int(parts[0]), int(parts[1]), str(parts[4]),
+ threshold=t, x2=parts[2], y2=parts[3])
+ else:
+ raise Exception(
+ "Unsupported coordinate specification:\n"
+ "path: %s" % path % "line: %d" % index)

emvis/tests/test_dualimagelistview.py

@@ -16,92 +16,43 @@ def getDataPaths(self):
  ]
 
  def createView(self):
- tool_params1 = [
- [
- {
- 'name': 'threshold',
- 'type': 'float',
- 'value': 0.55,
- 'label': 'Quality threshold',
- 'help': 'If this is ... bla bla bla',
- 'display': 'default'
- },
- {
- 'name': 'thresholdBool',
- 'type': 'bool',
- 'value': True,
- 'label': 'Quality checked',
- 'help': 'If this is a boolean param'
- }
- ],
- [
- {
- 'name': 'threshold543',
- 'type': 'float',
- 'value': 0.67,
- 'label': 'Quality',
- 'help': 'If this is ... bla bla bla',
- 'display': 'default'
- },
- {
- 'name': 'threshold',
- 'type': 'float',
- 'value': 14.55,
- 'label': 'Quality threshold2',
- 'help': 'If this is ... bla bla bla',
- 'display': 'default'
- }
- ],
- {
- 'name': 'threshold2',
- 'type': 'string',
- 'value': 'Explanation text',
- 'label': 'Threshold ex',
- 'help': 'If this is ... bla bla bla 2',
- 'display': 'default'
- },
- {
- 'name': 'text',
- 'type': 'string',
- 'value': 'Text example',
- 'label': 'Text',
- 'help': 'If this is ... bla bla bla for text'
- },
- {
- 'name': 'threshold4',
- 'type': 'float',
- 'value': 1.5,
- 'label': 'Quality',
- 'help': 'If this is ... bla bla bla for quality'
- },
- {
- 'name': 'picking-method',
- 'type': 'enum', # or 'int' or 'string' or 'enum',
- 'choices': ['LoG', 'Swarm', 'SVM'],
- 'value': 1, # values in enum are int, in this case it is 'LoG'
- 'label': 'Picking method',
- 'help': 'Select the picking strategy that you want to use. ',
- # display should be optional, for most params, a textbox is the
- # default
- # for enum, a combobox is the default, other options could be
- # sliders
- 'display': 'combo' # or 'combo' or 'vlist' or 'hlist' or
- # 'slider'
- },
- {
- 'name': 'threshold3',
- 'type': 'bool',
- 'value': True,
- 'label': 'Checked',
- 'help': 'If this is a boolean param'
- }
- ]
+ Param = dv.models.Param
+ brightness = Param('brightness', 'int', value=50, display='slider',
+ range=(1, 100), label='Brightness',
+ help='Adjust image brightness.')
+
+ threshold = Param('threshold', 'float', value=0.55,
+ label='Quality threshold',
+ help='If this is...bla bla bla')
+ thresholdBool = Param('threshold', 'bool', value=True,
+ label='Quality checked',
+ help='If this is a boolean param')
+
+ threshold5 = Param('threshold5', 'string', value='Another text',
+ label='Another text example',
+ help='Showing more text')
+
+ threshold6 = Param('threshold6', 'float', value=1.5,
+ label='Another float',
+ help='Just another float example')
+
+ apply = Param('apply', 'button', label='Operation1')
+
+ form = dv.models.Form([
+ brightness,
+ [threshold, thresholdBool],
+ threshold5,
+ threshold6,
+ [apply]
+ ])
+
  return dv.views.DualImageListView(
  emv.models.ModelsFactory.createListModel(self.getDataPaths()),
- options=tool_params1, method=printFunc)
+ form=form, method=printFunc)
 
 
 def printFunc(*args):
+ print('Example function. Print the arguments:')
  print(args)