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):
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 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 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):
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()
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()
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,
status = 'waiting',
view_error = "Not yet plotted")
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,
status = 'waiting',
view_error = "Not yet plotted")
self.workflow.workflow.append(wi)
op = plugin.get_operation()
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 = 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,
status = 'waiting',
view_error = "Not yet plotted")
self.workflow.workflow.append(wi)
self.workflow.selected = wi
self.workflow.wi_waitfor(wi, 'status', "valid")
plugin = TablePlugin()
self.view = view = plugin.get_view()
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', '')