def add_operation(self, operation):
# add the new operation after the selected workflow item or at the end
# of the workflow if no wi is selected
# make a new workflow item
wi = WorkflowItem(operation = operation,
deletable = (operation.id != "edu.mit.synbio.cytoflow.operations.import"))
# they say in Python you should ask for forgiveness instead of permission
try:
wi.default_view = operation.default_view()
wi.views.append(wi.default_view)
except AttributeError:
pass
if self.workflow and self.selected:
idx = self.workflow.index(self.selected) + 1
elif self.workflow:
idx = len(self.workflow)
else:
idx = 0
# the add_remove_items handler takes care of updating the linked list
self.workflow.insert(idx, wi)
# select (open) the new workflow item
self.selected = wi
if wi.default_view:
wi.current_view = wi.default_view
def setUp(self):
super().setUp()
plugin = ChannelStatisticPlugin()
op = plugin.get_operation()
op.name = "Count"
op.channel = "Y2-A"
op.statistic_name = "Count"
op.by = ['Dox', 'Well']
wi = WorkflowItem(operation=op)
self.workflow.workflow.append(wi)
plugin = TransformStatisticPlugin()
self.op = op = plugin.get_operation()
op.name = "Mean"
op.statistic = ("Count", "Count")
op.statistic_name = "Count"
op.by = ["Dox"]
op.subset_list.append(CategorySubset(name="Well", values=["A", "B"]))
self.wi = wi = WorkflowItem(operation=op,
status='waiting',
view_error="Not yet plotted")
self.workflow.workflow.append(wi)
self.workflow.selected = wi
self.workflow.wi_waitfor(wi, 'status', "valid")
def activated(self):
# add an import plugin
plugin = ImportPlugin()
wi = WorkflowItem(task = self)
wi.operation = plugin.get_operation()
self.model.workflow.append(wi)
self.model.selected = wi
# if we're debugging, add a few data bits
if self.debug:
from cytoflow import Tube
wi.operation.conditions["Dox"] = "log"
tube1 = Tube(file = "../cytoflow/tests/data/Plate01/CFP_Well_A4.fcs",
conditions = {"Dox" : 0.1})
tube2 = Tube(file = "../cytoflow/tests/data/Plate01/RFP_Well_A3.fcs",
conditions = {"Dox" : 1.0})
wi.operation.tubes.append(tube1)
wi.operation.tubes.append(tube2)
self.add_operation('edu.mit.synbio.cytoflowgui.op_plugins.hlog')
self.model.selected.operation.channels = ["V2-A", "Y2-A"]
self.model.selected.operation.name = "H"
self.add_operation('edu.mit.synbio.cytoflowgui.op_plugins.threshold')
self.model.selected.operation.channel = "Y2-A"
self.model.selected.operation.threshold = 2000
self.model.selected.operation.name = "T"
def activated(self):
# add an import plugin
plugin = ImportPlugin()
wi = WorkflowItem(task=self)
wi.operation = plugin.get_operation()
self.model.workflow.append(wi)
self.model.selected = wi
# if we're debugging, add a few data bits
if self.debug:
from cytoflow import Tube
wi.operation.conditions["Dox"] = "log"
tube1 = Tube(file="../cytoflow/tests/data/Plate01/CFP_Well_A4.fcs",
conditions={"Dox": 0.1})
tube2 = Tube(file="../cytoflow/tests/data/Plate01/RFP_Well_A3.fcs",
conditions={"Dox": 1.0})
wi.operation.tubes.append(tube1)
wi.operation.tubes.append(tube2)
self.add_operation(
'edu.mit.synbio.cytoflowgui.op_plugins.threshold')
self.model.selected.operation.channel = "Y2-A"
self.model.selected.operation.threshold = 2000
self.model.selected.operation.name = "T"
def setUp(self):
ImportedDataTest.setUp(self)
plugin = ChannelStatisticPlugin()
op = plugin.get_operation()
op.name = "Count"
op.channel = "Y2-A"
op.statistic_name = "Count"
op.by = ['Dox', 'Well']
wi = WorkflowItem(operation=op)
self.workflow.workflow.append(wi)
self.assertTrue(wait_for(wi, 'status', lambda v: v == 'valid', 30))
plugin = TransformStatisticPlugin()
self.op = op = plugin.get_operation()
op.name = "Mean"
op.statistic = ("Count", "Count")
op.statistic_name = "Count"
op.by = ["Dox"]
op.subset_list.append(CategorySubset(name="Well", values=["A", "B"]))
self.wi = wi = WorkflowItem(operation=op)
self.workflow.workflow.append(wi)
self.workflow.selected = wi
self.assertTrue(wait_for(wi, 'status', lambda v: v == 'valid', 30))
def setUp(self):
TasbeTest.setUp(self)
plugin = ThresholdPlugin()
op = plugin.get_operation()
op.name = "Morpho"
op.channel = "FSC-A"
op.threshold = 100000
wi = WorkflowItem(operation=op)
self.workflow.workflow.append(wi)
self.assertTrue(wait_for(wi, 'status', lambda v: v == 'valid', 30))
plugin = AutofluorescencePlugin()
self.op = op = plugin.get_operation()
self.cwd = os.path.dirname(os.path.abspath(__file__))
op.blank_file = self.cwd + "/../../cytoflow/tests/data/tasbe/blank.fcs"
op.channels = ["FITC-A", "Pacific Blue-A", "PE-Tx-Red-YG-A"]
op.subset_list.append(BoolSubset(name="Morpho"))
op.subset_list[0].selected_t = True
self.wi = wi = WorkflowItem(operation=op)
wi.default_view = self.op.default_view()
wi.view_error = "Not yet plotted"
wi.views.append(self.wi.default_view)
self.workflow.workflow.append(wi)
self.workflow.selected = self.wi
# run the estimate
op.do_estimate = True
self.assertTrue(wait_for(wi, 'status', lambda v: v == 'valid', 30))
def setUp(self):
super().setUp()
plugin = ImportPlugin()
op = plugin.get_operation()
from cytoflow import Tube
self.cwd = os.path.dirname(os.path.abspath(__file__))
tube = Tube(file=self.cwd + "/../../cytoflow/tests/data/tasbe/rby.fcs")
op.tubes = [tube]
wi = WorkflowItem(operation=op,
status="waiting",
view_error="Not yet plotted")
self.workflow.workflow.append(wi)
op.do_estimate = True
self.workflow.wi_waitfor(wi, 'status', 'valid')
self.assertTrue(
self.workflow.remote_eval("self.workflow[0].result is not None"))
plugin = ThresholdPlugin()
op = plugin.get_operation()
op.name = "Morpho"
op.channel = "FSC-A"
op.threshold = 100000
wi = WorkflowItem(operation=op, status='waiting')
self.workflow.workflow.append(wi)
self.workflow.wi_waitfor(wi, 'status', 'valid')
def add_operation(self, op_id):
# first, find the matching plugin
plugin = next((x for x in self.op_plugins if x.id == op_id))
# next, get an operation
op = plugin.get_operation()
# make a new workflow item
wi = WorkflowItem(operation = op,
deletable = (op_id != 'edu.mit.synbio.cytoflowgui.op_plugins.import'))
# if the op has a default view, add it to the wi
try:
wi.default_view = op.default_view()
wi.views.append(wi.default_view)
wi.current_view = wi.default_view
except AttributeError:
pass
# figure out where to add it
if self.model.selected:
idx = self.model.workflow.index(self.model.selected) + 1
else:
idx = len(self.model.workflow)
# the add_remove_items handler takes care of updating the linked list
self.model.workflow.insert(idx, wi)
# and make sure to actually select the new wi
self.model.selected = wi
def setUp(self):
TasbeTest.setUp(self)
plugin = ThresholdPlugin()
op = plugin.get_operation()
op.name = "Morpho"
op.channel = "FSC-A"
op.threshold = 100000
wi = WorkflowItem(operation=op)
self.workflow.workflow.append(wi)
self.assertTrue(wait_for(wi, 'status', lambda v: v == 'valid', 30))
plugin = TasbePlugin()
self.op = op = plugin.get_operation()
self.cwd = os.path.dirname(os.path.abspath(__file__))
self.wi = wi = WorkflowItem(operation=op)
wi.default_view = self.op.default_view()
wi.view_error = "Not yet plotted"
wi.views.append(self.wi.default_view)
self.workflow.workflow.append(wi)
self.workflow.selected = self.wi
op.channels = ["FITC-A", "Pacific Blue-A", "PE-Tx-Red-YG-A"]
op.blank_file = self.cwd + "/../../cytoflow/tests/data/tasbe/blank.fcs"
op.bleedthrough_list = [
_BleedthroughControl(channel="FITC-A",
file=self.cwd +
"/../../cytoflow/tests/data/tasbe/eyfp.fcs"),
_BleedthroughControl(channel="Pacific Blue-A",
file=self.cwd +
"/../../cytoflow/tests/data/tasbe/ebfp.fcs"),
_BleedthroughControl(channel="PE-Tx-Red-YG-A",
file=self.cwd +
"/../../cytoflow/tests/data/tasbe/mkate.fcs")
]
op.beads_name = "Spherotech RCP-30-5A Lot AG01, AF02, AD04 and AAE01"
op.beads_file = self.cwd + "/../../cytoflow/tests/data/tasbe/beads.fcs"
op.beads_unit = "MEFL"
op.to_channel = "FITC-A"
self.op.translation_list[
0].file = self.cwd + "/../../cytoflow/tests/data/tasbe/rby.fcs"
self.op.translation_list[
1].file = self.cwd + "/../../cytoflow/tests/data/tasbe/rby.fcs"
op.subset_list.append(BoolSubset(name="Morpho"))
op.subset_list[0].selected_t = True
# run the estimate
op.do_estimate = True
self.assertTrue(wait_for(wi, 'status', lambda v: v == 'valid', 30))
def on_new(self):
self.model.workflow = []
# add an import plugin
plugin = ImportPlugin()
wi = WorkflowItem(task = self)
wi.operation = plugin.get_operation()
self.model.workflow.append(wi)
self.model.selected = wi
def on_new(self):
self.model.workflow = []
# add an import plugin
plugin = ImportPlugin()
wi = WorkflowItem(task=self)
wi.operation = plugin.get_operation()
self.model.workflow.append(wi)
self.model.selected = wi
def setUp(self):
super().setUp()
stats_plugin = ChannelStatisticPlugin()
stats_op_3 = stats_plugin.get_operation()
stats_op_3.name = "MeanByDoxIP2"
stats_op_3.channel = "B1-A"
stats_op_3.statistic_name = "Geom.Mean"
stats_op_3.by = ['Dox', 'IP']
stats_op_3.subset_list.append(CategorySubset(name = "Well",
values = ['A', 'B']))
stats_op_3.subset_list.append(RangeSubset(name = "Dox",
values = [1.0, 10.0, 100.0]))
stats_op_3.subset_list.append(RangeSubset(name = "IP",
values = [1.0, 10.0]))
stats_wi_3 = WorkflowItem(operation = stats_op_3,
status = "waiting",
view_error = "Not yet plotted")
self.workflow.workflow.append(stats_wi_3)
self.workflow.wi_waitfor(stats_wi_3, 'status', 'valid')
stats_op_4 = stats_plugin.get_operation()
stats_op_4.name = "SDByDoxIP2"
stats_op_4.channel = "B1-A"
stats_op_4.statistic_name = "Geom.SD"
stats_op_4.by = ['Dox', 'IP']
stats_op_4.subset_list.append(CategorySubset(name = "Well",
values = ['A', 'B']))
stats_op_4.subset_list.append(RangeSubset(name = "Dox",
values = [1.0, 10.0, 100.0]))
stats_op_4.subset_list.append(RangeSubset(name = "IP",
values = [1.0, 10.0]))
stats_wi_4 = WorkflowItem(operation = stats_op_4,
status = "waiting",
view_error = "Not yet plotted")
self.workflow.workflow.append(stats_wi_4)
self.workflow.wi_waitfor(stats_wi_4, 'status', 'valid')
self.wi = wi = self.workflow.workflow[-1]
plugin = Stats2DPlugin()
self.view = view = plugin.get_view()
wi.views.append(view)
wi.current_view = view
super().setUpView()
self.workflow.selected = wi
def setUp(self):
super().setUp()
plugin = BeadCalibrationPlugin()
self.op = op = plugin.get_operation()
self.cwd = os.path.dirname(os.path.abspath(__file__))
op.beads_name = "Spherotech RCP-30-5A Lot AG01, AF02, AD04 and AAE01"
op.beads_file = self.cwd + "/../../cytoflow/tests/data/tasbe/beads.fcs"
op.units_list = [
_Unit(channel="FITC-A", unit="MEFL"),
_Unit(channel="Pacific Blue-A", unit="MEBFP")
]
self.wi = wi = WorkflowItem(operation=op,
status='waiting',
view_error="Not yet plotted")
wi.default_view = self.op.default_view()
wi.views.append(self.wi.default_view)
self.workflow.workflow.append(wi)
self.workflow.selected = self.wi
# run the estimate
op.do_estimate = True
self.workflow.wi_waitfor(wi, 'status', "valid")
def setUp(self):
super().setUp()
plugin = PolygonPlugin()
self.op = op = plugin.get_operation()
op.name = "Poly"
op.xchannel = "Y2-A"
op.xscale = "logicle"
op.ychannel = "V2-A"
op.yscale = "logicle"
op.vertices = [(23.411982294776319, 5158.7027015021222),
(102.22182270573683, 23124.0588433874530),
(510.94519955277201, 23124.0588433874530),
(1089.5215641232173, 3800.3424832180476),
(340.56382570202402, 801.98947404942271),
(65.42597937575897, 1119.3133482602157)]
self.wi = wi = WorkflowItem(operation = op,
status = 'waiting',
view_error = "Not yet plotted")
self.view = view = wi.default_view = op.default_view()
view.subset_list.append(CategorySubset(name = "Well", values = ["A", "B"]))
wi.view_error = "Not yet plotted"
wi.views.append(self.wi.default_view)
self.wi.current_view = self.wi.default_view
self.workflow.workflow.append(wi)
self.workflow.selected = wi
self.workflow.wi_waitfor(self.wi, 'status', 'valid')
def setUp(self):
super().setUp()
stats_plugin = ChannelStatisticPlugin()
stats_op = stats_plugin.get_operation()
stats_op.name = "MeanByDoxWell"
stats_op.channel = "Y2-A"
stats_op.statistic_name = "Geom.Mean"
stats_op.by = ['Dox', 'Well']
stats_op.subset_list.append(CategorySubset(name = "Well",
values = ['A', 'B']))
stats_op.subset_list.append(RangeSubset(name = "Dox",
values = [1.0, 10.0, 100.0]))
stats_op.subset_list.append(RangeSubset(name = "IP",
values = [1.0, 10.0]))
stats_wi = WorkflowItem(operation = stats_op,
status = "waiting",
view_error = "Not yet plotted")
self.workflow.workflow.append(stats_wi)
self.workflow.wi_waitfor(stats_wi, 'status', 'valid')
self.wi = wi = self.workflow.workflow[-1]
self.op = self.wi.operation
self.workflow.selected = wi
def setUp(self):
super().setUp()
plugin = Range2DPlugin()
self.op = op = plugin.get_operation()
op.name = "Range2D"
op.xchannel = "Y2-A"
op.xlow = 100
op.xhigh = 1000
op.ychannel = "V2-A"
op.ylow = 1000
op.yhigh = 10000
self.wi = wi = WorkflowItem(operation = op,
status = 'waiting',
view_error = "Not yet plotted")
self.view = wi.default_view = op.default_view()
wi.views.append(self.wi.default_view)
self.wi.current_view = self.wi.default_view
self.workflow.workflow.append(wi)
self.workflow.selected = wi
self.workflow.wi_waitfor(self.wi, 'status', 'valid')
def setUp(self):
ImportedDataTest.setUp(self)
plugin = PCAPlugin()
self.op = op = plugin.get_operation()
op.name = "PCA"
op.channels_list = [
_Channel(channel="V2-A", scale="log"),
_Channel(channel="V2-H", scale="log"),
_Channel(channel="Y2-A", scale="log"),
_Channel(channel="Y2-H", scale="log")
]
op.num_components = 2
op.subset_list.append(CategorySubset(name="Well", values=["A", "B"]))
self.wi = wi = WorkflowItem(operation=op)
self.workflow.workflow.append(wi)
self.workflow.selected = wi
# run estimate
op.do_estimate = True
self.assertTrue(wait_for(wi, 'status', lambda v: v == 'valid', 30))
def setUp(self):
ImportedDataTest.setUp(self)
plugin = FlowPeaksPlugin()
self.op = op = plugin.get_operation()
op.name = "FP"
op.xchannel = "V2-A"
op.ychannel = "Y2-A"
op.xscale = "logicle"
op.yscale = "logicle"
op.h0 = 0.5
op.subset_list.append(CategorySubset(name="Well", values=["A", "B"]))
self.wi = wi = WorkflowItem(operation=op)
wi.default_view = op.default_view()
wi.view_error = "Not yet plotted"
wi.views.append(self.wi.default_view)
self.workflow.workflow.append(wi)
self.workflow.selected = wi
# run estimate
op.do_estimate = True
self.assertTrue(wait_for(wi, 'status', lambda v: v == 'valid', 120))
def setUp(self):
super().setUp()
plugin = KMeansPlugin()
self.op = op = plugin.get_operation()
op.name = "KM"
op.xchannel = "V2-A"
op.ychannel = "Y2-A"
op.xscale = "logicle"
op.yscale = "logicle"
op.num_clusters = 2
op.subset_list.append(CategorySubset(name="Well", values=['A', 'B']))
op.subset_list.append(
RangeSubset(name="Dox", values=[0.0, 10.0, 100.0]))
self.wi = wi = WorkflowItem(operation=op,
status='waiting',
view_error="Not yet plotted")
wi.default_view = op.default_view()
wi.views.append(self.wi.default_view)
self.workflow.workflow.append(wi)
self.workflow.selected = wi
# run estimate
op.do_estimate = True
self.workflow.wi_waitfor(self.wi, 'status', 'valid')
def setUp(self):
super().setUp()
plugin = ColorTranslationPlugin()
self.op = op = plugin.get_operation()
self.cwd = os.path.dirname(os.path.abspath(__file__))
self.rby_file = self.cwd + "/../../cytoflow/tests/data/tasbe/rby.fcs"
op.controls_list = [
_Control(from_channel="Pacific Blue-A",
to_channel="FITC-A",
file=self.rby_file)
]
# op.channels = ["FITC-A", "Pacific Blue-A", "PE-Tx-Red-YG-A"]
op.subset_list.append(BoolSubset(name="Morpho"))
op.subset_list[0].selected_t = True
self.wi = wi = WorkflowItem(operation=op,
status='waiting',
view_error="Not yet plotted")
wi.default_view = self.op.default_view()
wi.views.append(self.wi.default_view)
self.workflow.workflow.append(wi)
self.workflow.selected = self.wi
# run the estimate
op.do_estimate = True
self.workflow.wi_waitfor(self.wi, 'status', 'valid')
def setUp(self):
super().setUp()
plugin = BleedthroughLinearPlugin()
self.op = op = plugin.get_operation()
self.cwd = os.path.dirname(os.path.abspath(__file__))
op.controls_list = [
_Control(channel="FITC-A",
file=self.cwd +
'/../../cytoflow/tests/data/tasbe/eyfp.fcs'),
_Control(channel="PE-Tx-Red-YG-A",
file=self.cwd +
'/../../cytoflow/tests/data/tasbe/mkate.fcs'),
_Control(channel="Pacific Blue-A",
file=self.cwd +
'/../../cytoflow/tests/data/tasbe/ebfp.fcs')
]
op.subset_list.append(BoolSubset(name="Morpho"))
op.subset_list[0].selected_t = True
self.wi = wi = WorkflowItem(operation=op,
status='waiting',
view_error="Not yet plotted")
wi.default_view = self.op.default_view()
wi.views.append(self.wi.default_view)
self.workflow.workflow.append(wi)
self.workflow.selected = self.wi
# run the estimate
op.do_estimate = True
self.workflow.wi_waitfor(self.wi, 'status', 'valid')
def setUp(self):
super().setUp()
plugin = ThresholdPlugin()
self.op = op = plugin.get_operation()
op.name = "Thresh"
op.channel = "Y2-A"
op.threshold = 1000
self.wi = wi = WorkflowItem(operation=op,
status='waiting',
view_error="Not yet plotted")
self.view = view = wi.default_view = op.default_view()
view.subset_list.append(CategorySubset(name="Well", values=["A", "B"]))
wi.view_error = "Not yet plotted"
wi.views.append(self.wi.default_view)
self.wi.current_view = self.wi.default_view
self.workflow.workflow.append(wi)
self.workflow.selected = wi
self.workflow.wi_waitfor(wi, 'view_error', "")
self.workflow.wi_waitfor(wi, 'status', "valid")
def setUp(self):
super().setUp()
plugin = GaussianMixture1DPlugin()
self.op = op = plugin.get_operation()
op.name = "Gauss"
op.channel = "V2-A"
op.channel_scale = "logicle"
op.num_components = 2
op.subset_list.append(CategorySubset(name="Well", values=["A", "B"]))
op.subset_list.append(
RangeSubset(name="Dox", values=[0.0, 10.0, 100.0]))
self.wi = wi = WorkflowItem(operation=op,
status='waiting',
view_error="Not yet plotted")
wi.default_view = op.default_view()
wi.views.append(self.wi.default_view)
self.workflow.workflow.append(wi)
self.workflow.selected = wi
# run estimate
op.do_estimate = True
self.workflow.wi_waitfor(self.wi, 'status', 'valid')
def setUp(self):
super().setUp()
plugin = PCAPlugin()
self.op = op = plugin.get_operation()
op.name = "PCA"
op.channels_list = [_Channel(channel = "V2-A", scale = "log"),
_Channel(channel = "V2-H", scale = "log"),
_Channel(channel = "Y2-A", scale = "log"),
_Channel(channel = "Y2-H", scale = "log")]
op.num_components = 2
op.subset_list.append(CategorySubset(name = "Well",
values = ['A', 'B']))
op.subset_list.append(RangeSubset(name = "Dox",
values = [0.0, 10.0, 100.0]))
self.wi = wi = WorkflowItem(operation = op,
status = 'waiting',
view_error = "Not yet plotted")
self.workflow.workflow.append(wi)
self.workflow.selected = wi
# run estimate
op.do_estimate = True
self.workflow.wi_waitfor(self.wi, 'status', 'valid')
def setUp(self):
ImportedDataTest.setUp(self)
plugin = Range2DPlugin()
self.op = op = plugin.get_operation()
op.name = "Range2D"
op.xchannel = "Y2-A"
op.xlow = 100
op.xhigh = 1000
op.ychannel = "V2-A"
op.ylow = 1000
op.yhigh = 10000
self.wi = wi = WorkflowItem(operation=op)
self.view = view = wi.default_view = op.default_view()
view.subset_list.append(CategorySubset(name="Well", values=["A", "B"]))
wi.view_error = "Not yet plotted"
wi.views.append(self.wi.default_view)
self.wi.current_view = self.wi.default_view
self.workflow.workflow.append(wi)
self.workflow.selected = wi
self.assertTrue(wait_for(self.wi, 'view_error', lambda v: v == "", 30))
self.assertTrue(
wait_for(self.wi, 'status', lambda v: v == 'valid', 130))
def setUp(self):
ImportedDataTest.setUp(self)
plugin = ChannelStatisticPlugin()
op = plugin.get_operation()
op.name = "MeanByDox"
op.channel = "Y2-A"
op.statistic_name = "Geom.SD"
op.by = ['Dox']
wi = WorkflowItem(operation=op)
self.workflow.workflow.append(wi)
op = plugin.get_operation()
op.name = "MeanByDoxAndWell"
op.channel = "Y2-A"
op.statistic_name = "Geom.SD"
op.by = ['Dox', 'Well']
wi = WorkflowItem(operation=op)
self.workflow.workflow.append(wi)
op = plugin.get_operation()
op.name = "MeanByDox"
op.channel = "Y2-A"
op.statistic_name = "Geom.Mean"
op.by = ['Dox']
self.wi = wi = WorkflowItem(operation=op)
self.workflow.workflow.append(wi)
op = plugin.get_operation()
op.name = "MeanByDoxAndWell"
op.channel = "Y2-A"
op.statistic_name = "Geom.Mean"
op.by = ['Dox', 'Well']
self.wi = wi = WorkflowItem(operation=op)
self.workflow.workflow.append(wi)
self.workflow.selected = wi
self.assertTrue(wait_for(wi, 'status', lambda v: v == 'valid', 10))
plugin = TablePlugin()
self.view = view = plugin.get_view()
view.statistic = ("MeanByDox", "Geom.Mean")
view.row_facet = "Dox"
self.workflow.remote_exec("self.workflow[-1].view_error = 'waiting'")
self.assertTrue(
wait_for(self.wi, 'view_error', lambda v: v == "waiting", 30))
wi.views.append(view)
wi.current_view = view
self.workflow.selected = wi
self.assertTrue(wait_for(self.wi, 'view_error', lambda v: v == "", 30))
def activated(self):
self.model.backup_workflow = self.model.workflow
self.model.workflow = []
self.model.modified = False
# add the op
self.op = TasbeCalibrationOp()
# make a new workflow item
wi = WorkflowItem(operation=self.op, deletable=False)
wi.default_view = self.op.default_view()
wi.views.append(wi.default_view)
wi.current_view = wi.default_view
self.model.workflow.append(wi)
self.model.selected = wi
self.help_pane.html = self.op.get_help()
def setUp(self):
ImportedDataTest.setUp(self)
plugin = ChannelStatisticPlugin()
op = plugin.get_operation()
op.name = "MeanByDox"
op.channel = "Y2-A"
op.statistic_name = "Geom.SD"
op.by = ['Dox', 'Well']
wi = WorkflowItem(operation=op)
self.workflow.workflow.append(wi)
op = plugin.get_operation()
op.name = "MeanByDox"
op.channel = "Y2-A"
op.statistic_name = "Geom.Mean"
op.by = ['Dox', 'Well']
op.subset_list.append(CategorySubset(name="Well", values=["A", "B"]))
self.wi = wi = WorkflowItem(operation=op)
self.workflow.workflow.append(wi)
self.workflow.selected = wi
self.assertTrue(wait_for(wi, 'status', lambda v: v == 'valid', 10))
plugin = Stats1DPlugin()
self.view = view = plugin.get_view()
view.statistic = ("MeanByDox", "Geom.Mean")
view.variable = "Dox"
view.huefacet = "Well"
self.workflow.remote_exec("self.workflow[-1].view_error = 'waiting'")
self.assertTrue(
wait_for(self.wi, 'view_error', lambda v: v == "waiting", 5))
wi.views.append(view)
wi.current_view = view
self.workflow.selected = wi
self.assertTrue(wait_for(self.wi, 'view_error', lambda v: v == "", 5))
def setUp(self):
super().setUp()
self.op = op = TasbeCalibrationOp()
self.cwd = os.path.dirname(os.path.abspath(__file__))
self.wi = wi = WorkflowItem(operation=op,
status='waiting',
view_error="Not yet plotted")
wi.default_view = self.op.default_view()
wi.views.append(self.wi.default_view)
self.workflow.workflow.append(wi)
self.workflow.selected = self.wi
op.blank_file = self.cwd + "/../../cytoflow/tests/data/tasbe/blank.fcs"
op.fsc_channel = "FSC-A"
op.ssc_channel = "SSC-A"
op._polygon_op.vertices = [(72417, 499), (74598, 1499), (118743, 3376),
(216547, 6166), (246258, 4543),
(237880, 1973), (139102, 872), (87822, 519)]
op.channels = ["FITC-A", "Pacific Blue-A", "PE-Tx-Red-YG-A"]
op.bleedthrough_list = [
_BleedthroughControl(channel="FITC-A",
file=self.cwd +
"/../../cytoflow/tests/data/tasbe/eyfp.fcs"),
_BleedthroughControl(channel="Pacific Blue-A",
file=self.cwd +
"/../../cytoflow/tests/data/tasbe/ebfp.fcs"),
_BleedthroughControl(channel="PE-Tx-Red-YG-A",
file=self.cwd +
"/../../cytoflow/tests/data/tasbe/mkate.fcs")
]
op.beads_name = "Spherotech RCP-30-5A Lot AG01, AF02, AD04 and AAE01"
op.beads_file = self.cwd + "/../../cytoflow/tests/data/tasbe/beads.fcs"
op.units_list = [
_Unit(channel="FITC-A", unit="MEFL"),
_Unit(channel="Pacific Blue-A", unit="MEBFP"),
_Unit(channel="PE-Tx-Red-YG-A", unit="MEPTR")
]
op.do_color_translation = False
op.output_directory = tempfile.mkdtemp()
# run the estimate
self.workflow.remote_exec("pass")
op.valid_model = False
op.do_estimate = True
wait_for_condition(lambda v: v.valid_model == True, self.op,
'valid_model', 30)
def add_operation(self, op_id):
# first, find the matching plugin
plugin = next((x for x in self.op_plugins if x.id == op_id))
# default to inserting at the end of the list if none selected
after = self.model.selected
if after is None:
after = self.model.workflow[-1]
idx = self.model.workflow.index(after)
wi = WorkflowItem(task = self)
wi.operation = plugin.get_operation()
wi.next = after.next
after.next = wi
wi.previous = after
if wi.next:
wi.next.previous = wi
self.model.workflow.insert(idx+1, wi)
# set up the default view
wi.default_view = plugin.get_default_view(wi.operation)
if wi.default_view is not None:
wi.default_view.handler = \
wi.default_view.handler_factory(model = wi.default_view, wi = wi.previous)
wi.views.append(wi.default_view)
# select (open) the new workflow item
self.model.selected = wi
if wi.default_view:
wi.current_view = wi.default_view
# invalidate everything following
self.operation_parameters_updated()
def setUp(self):
TasbeTest.setUp(self)
plugin = ThresholdPlugin()
op = plugin.get_operation()
op.name = "Morpho"
op.channel = "FSC-A"
op.threshold = 100000
wi = WorkflowItem(operation = op)
self.workflow.workflow.append(wi)
self.assertTrue(wait_for(wi, 'status', lambda v: v == 'valid', 5))
plugin = BleedthroughLinearPlugin()
self.op = op = plugin.get_operation()
self.cwd = os.path.dirname(os.path.abspath(__file__))
op.controls_list = [_Control(channel = "FITC-A",
file = self.cwd + '/../../cytoflow/tests/data/tasbe/eyfp.fcs'),
_Control(channel = "PE-Tx-Red-YG-A",
file = self.cwd + '/../../cytoflow/tests/data/tasbe/mkate.fcs'),
_Control(channel = "Pacific Blue-A",
file = self.cwd + '/../../cytoflow/tests/data/tasbe/ebfp.fcs')]
op.subset_list.append(BoolSubset(name = "Morpho"))
op.subset_list[0].selected_t = True
self.wi = wi = WorkflowItem(operation = op)
wi.default_view = self.op.default_view()
wi.view_error = "Not yet plotted"
wi.views.append(self.wi.default_view)
self.workflow.workflow.append(wi)
self.workflow.selected = self.wi
# run the estimate
op.do_estimate = True
self.assertTrue(wait_for(wi, 'status', lambda v: v == 'valid', 30))
def setUp(self):
WorkflowTest.setUp(self)
plugin = ImportPlugin()
op = plugin.get_operation()
from cytoflow import Tube
self.cwd = os.path.dirname(os.path.abspath(__file__))
tube = Tube(file = self.cwd + "/../../cytoflow/tests/data/tasbe/rby.fcs")
op.tubes = [tube]
wi = WorkflowItem(operation = op,
view_error = "Not yet plotted")
self.workflow.workflow.append(wi)
self.assertTrue(wait_for(wi, 'status', lambda v: v == 'valid', 5))
self.assertTrue(self.workflow.remote_eval("self.workflow[0].result is not None"))
def setUp(self):
ImportedDataTest.setUp(self)
plugin = BinningPlugin()
self.op = op = plugin.get_operation()
op.name = "Bin"
op.channel = "V2-A"
op.scale = "log"
op.bin_width = 0.2
self.wi = wi = WorkflowItem(operation=op)
wi.default_view = op.default_view()
wi.view_error = "Not yet plotted"
wi.views.append(self.wi.default_view)
self.workflow.workflow.append(wi)
self.workflow.selected = wi
self.assertTrue(wait_for(wi, 'status', lambda v: v == 'valid', 10))
def setUp(self):
super().setUp()
plugin = BinningPlugin()
self.op = op = plugin.get_operation()
op.name = "Bin"
op.channel = "V2-A"
op.scale = "log"
op.bin_width = 0.2
self.wi = wi = WorkflowItem(operation=op,
status='waiting',
view_error="Not yet plotted")
self.view = wi.default_view = op.default_view()
wi.views.append(self.wi.default_view)
self.workflow.workflow.append(wi)
self.workflow.selected = wi
self.workflow.wi_waitfor(wi, 'status', "valid")
