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.selected = wi
self.workflow.wi_waitfor(wi, 'status', 'valid')
def setUp(self):
super().setUp()
op = ChannelStatisticWorkflowOp()
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.op = op = TransformStatisticWorkflowOp()
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 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]
self.view = view = Stats2DWorkflowView()
wi.views.append(view)
wi.current_view = view
super().setUpView()
self.workflow.selected = wi
self.workflow.wi_waitfor(self.wi, 'view_error', '')
def setUp(self):
super().setUp()
self.op = op = GaussianMixture2DWorkflowOp()
op.name = "Gauss"
op.xchannel = "V2-A"
op.ychannel = "Y2-A"
op.xscale = "logicle"
op.yscale = "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.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()
self.op = op = BleedthroughLinearWorkflowOp()
self.cwd = os.path.dirname(os.path.abspath(__file__))
op.controls_list = [BleedthroughControl(channel = "FITC-A",
file = self.cwd + '/../../cytoflow/tests/data/tasbe/eyfp.fcs'),
BleedthroughControl(channel = "PE-Tx-Red-YG-A",
file = self.cwd + '/../../cytoflow/tests/data/tasbe/mkate.fcs'),
BleedthroughControl(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.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()
self.op = op = PCAWorkflowOp()
op.name = "PCA"
op.channels_list = [
PCAChannel(channel="V2-A", scale="log"),
PCAChannel(channel="V2-H", scale="log"),
PCAChannel(channel="Y2-A", scale="log"),
PCAChannel(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):
super().setUp()
self.op = op = TasbeWorkflowOp()
self.cwd = os.path.dirname(os.path.abspath(__file__))
self.wi = wi = WorkflowItem(operation=op,
status='waiting',
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.do_color_translation = True
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.workflow.wi_waitfor(self.wi, 'status', 'valid')
def setUp(self):
super().setUp()
self.op = op = BinningWorkflowOp()
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")
wi.views.append(self.wi.default_view)
self.workflow.workflow.append(wi)
self.workflow.selected = wi
self.workflow.wi_waitfor(wi, 'status', "valid")
def setUp(self):
super().setUp()
self.op = op = AutofluorescenceWorkflowOp()
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,
status='waiting',
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.workflow.wi_waitfor(self.wi, 'status', 'valid')
def setUp(self):
super().setUp()
self.op = op = RangeWorkflowOp()
op.name = "Range"
op.channel = "Y2-A"
op.low = 100
op.high = 1000
self.wi = wi = WorkflowItem(operation=op,
status='waiting',
view_error="Not yet plotted")
self.view = wi.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(wi, 'view_error', "")
self.workflow.wi_waitfor(wi, 'status', "valid")
def setUp(self):
super().setUp()
self.op = op = RangeWorkflowOp()
op.name = "Range"
op.channel = "Y2-A"
op.low = 100
op.high = 1000
self.wi = wi = WorkflowItem(operation=op,
status='waiting',
view_error="Not yet plotted")
self.workflow.workflow.append(wi)
self.workflow.selected = wi
self.view = view = ViolinPlotWorkflowView()
wi.views.append(view)
wi.current_view = view
self.workflow.selected = self.wi
self.view.variable = "Range"
super().setUpView()
self.workflow.wi_waitfor(self.wi, 'view_error', '')
def setUp(self):
super().setUp()
stats_op = ChannelStatisticWorkflowOp()
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()
self.op = op = ThresholdWorkflowOp()
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
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()
self.op = op = BeadCalibrationWorkflowOp()
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 = [
BeadCalibrationUnit(channel="FITC-A", unit="MEFL"),
BeadCalibrationUnit(channel="Pacific Blue-A", unit="MEBFP")
]
self.wi = wi = WorkflowItem(operation=op,
status='waiting',
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.workflow.wi_waitfor(wi, 'status', "valid")
def setUp(self):
super().setUp()
import_plugin = ImportPlugin()
import_op = import_plugin.get_operation()
from cytoflow import Tube
import_op.conditions = {
"Dox": "float",
"IP": "float",
"Well": "category"
}
self.cwd = os.path.dirname(os.path.abspath(__file__))
tube1 = Tube(file=self.cwd +
"/../../cytoflow/tests/data/Plate01/CFP_Well_A4.fcs",
conditions={
"Dox": 1.0,
"IP": 1.0,
"Well": 'A'
})
tube2 = Tube(file=self.cwd +
"/../../cytoflow/tests/data/Plate01/RFP_Well_A3.fcs",
conditions={
"Dox": 1.0,
"IP": 10.0,
"Well": 'B'
})
tube3 = Tube(file=self.cwd +
"/../../cytoflow/tests/data/Plate01/YFP_Well_A7.fcs",
conditions={
"Dox": 10.0,
"IP": 1.0,
"Well": 'A'
})
tube4 = Tube(file=self.cwd +
"/../../cytoflow/tests/data/Plate01/CFP_Well_B4.fcs",
conditions={
"Dox": 10.0,
"IP": 10.0,
"Well": 'B'
})
tube5 = Tube(file=self.cwd +
"/../../cytoflow/tests/data/Plate01/RFP_Well_A6.fcs",
conditions={
"Dox": 100.0,
"IP": 1.0,
"Well": 'A'
})
tube6 = Tube(file=self.cwd +
"/../../cytoflow/tests/data/Plate01/YFP_Well_C7.fcs",
conditions={
"Dox": 100.0,
"IP": 100.0,
"Well": 'B'
})
import_op.tubes = [tube1, tube2, tube3, tube4, tube5, tube6]
wi = WorkflowItem(operation=import_op,
status="waiting",
view_error="Not yet plotted")
self.workflow.workflow.append(wi)
import_op.do_estimate = True
self.workflow.wi_waitfor(wi, 'status', 'valid')
self.assertTrue(
self.workflow.remote_eval("self.workflow[0].result is not None"))
stats_plugin = ChannelStatisticPlugin()
stats_op_1 = stats_plugin.get_operation()
stats_op_1.name = "MeanByDoxIP"
stats_op_1.channel = "Y2-A"
stats_op_1.statistic_name = "Geom.Mean"
stats_op_1.by = ['Dox', 'IP']
stats_op_1.subset_list.append(
CategorySubset(name="Well", values=['A', 'B']))
stats_op_1.subset_list.append(
RangeSubset(name="Dox", values=[1.0, 10.0, 100.0]))
stats_op_1.subset_list.append(
RangeSubset(name="IP", values=[1.0, 10.0]))
stats_wi_1 = WorkflowItem(operation=stats_op_1,
status="waiting",
view_error="Not yet plotted")
self.workflow.workflow.append(stats_wi_1)
self.workflow.wi_waitfor(stats_wi_1, 'status', 'valid')
stats_op_2 = stats_plugin.get_operation()
stats_op_2.name = "SDByDoxIP"
stats_op_2.channel = "Y2-A"
stats_op_2.statistic_name = "Geom.SD"
stats_op_2.by = ['Dox', 'IP']
stats_op_2.subset_list.append(
CategorySubset(name="Well", values=['A', 'B']))
stats_op_2.subset_list.append(
RangeSubset(name="Dox", values=[1.0, 10.0, 100.0]))
stats_op_2.subset_list.append(
RangeSubset(name="IP", values=[1.0, 10.0]))
stats_wi_2 = WorkflowItem(operation=stats_op_2,
status="waiting",
view_error="Not yet plotted")
self.workflow.workflow.append(stats_wi_2)
self.workflow.selected = stats_wi_2
self.workflow.wi_waitfor(stats_wi_2, 'status', 'valid')
def setUp(self):
super().setUp()
op = ChannelStatisticWorkflowOp()
op.name = "MeanByDox"
op.channel = "Y2-A"
op.statistic_name = "Geom.SD"
op.by = ['Dox']
wi = WorkflowItem(operation=op,
status='waiting',
view_error="Not yet plotted")
self.workflow.workflow.append(wi)
op = ChannelStatisticWorkflowOp()
op.name = "MeanByDoxAndWell"
op.channel = "Y2-A"
op.statistic_name = "Geom.SD"
op.by = ['Dox', 'Well']
wi = WorkflowItem(operation=op,
status='waiting',
view_error="Not yet plotted")
self.workflow.workflow.append(wi)
op = ChannelStatisticWorkflowOp()
op.name = "MeanByDox"
op.channel = "Y2-A"
op.statistic_name = "Geom.Mean"
op.by = ['Dox']
wi = WorkflowItem(operation=op,
status='waiting',
view_error="Not yet plotted")
self.workflow.workflow.append(wi)
op = ChannelStatisticWorkflowOp()
op.name = "MeanByDoxAndWell"
op.channel = "Y2-A"
op.statistic_name = "Geom.Mean"
op.by = ['Dox', 'Well']
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")
self.view = view = TableWorkflowView()
view.statistic = ("MeanByDox", "Geom.Mean")
view.row_facet = "Dox"
self.workflow.wi_sync(self.wi, 'view_error', 'waiting')
wi.views.append(view)
wi.current_view = view
self.workflow.selected = wi
self.workflow.wi_waitfor(self.wi, 'view_error', '')
