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 = 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()
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 = 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()
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 = 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):
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 = "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 = 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 = 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):
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):
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 setUpView(self):
super().setUpView()
self.view.subset_list.append(
CategorySubset(name="Well", values=['A', 'B']))
self.view.subset_list.append(
RangeSubset(name="Dox", values=[1.0, 10.0, 100.0]))
def testSubset(self):
self.workflow.wi_sync(self.wi, 'view_error', 'waiting')
self.view.subset_list.append(CategorySubset(name = "Well",
values = ['A', 'B']))
self.view.subset_list.append(RangeSubset(name = "Dox",
values = [0.0, 10.0, 100.0]))
self.view.subset_list[0].selected = ["A"]
self.workflow.wi_waitfor(self.wi, 'view_error', '')
def testAll(self):
self.workflow.remote_exec("self.workflow[0].view_error = 'waiting'")
self.assertTrue(
wait_for(self.wi, 'view_error', lambda v: v == "waiting", 30))
self.view.xscale = "log"
self.assertTrue(wait_for(self.wi, 'view_error', lambda v: v == "", 30))
self.workflow.remote_exec("self.workflow[0].view_error = 'waiting'")
self.assertTrue(
wait_for(self.wi, 'view_error', lambda v: v == "waiting", 30))
self.view.yscale = "logicle"
self.assertTrue(wait_for(self.wi, 'view_error', lambda v: v == "", 30))
self.workflow.remote_exec("self.workflow[0].view_error = 'waiting'")
self.assertTrue(
wait_for(self.wi, 'view_error', lambda v: v == "waiting", 30))
self.view.xfacet = "Dox"
self.assertTrue(wait_for(self.wi, 'view_error', lambda v: v == "", 30))
self.workflow.remote_exec("self.workflow[0].view_error = 'waiting'")
self.assertTrue(
wait_for(self.wi, 'view_error', lambda v: v == "waiting", 30))
self.view.yfacet = "Well"
self.assertTrue(wait_for(self.wi, 'view_error', lambda v: v == "", 30))
self.workflow.remote_exec("self.workflow[0].view_error = 'waiting'")
self.assertTrue(
wait_for(self.wi, 'view_error', lambda v: v == "waiting", 30))
self.view.xfacet = "Well"
self.view.yfacet = "Dox"
self.assertTrue(wait_for(self.wi, 'view_error', lambda v: v == "", 30))
self.workflow.remote_exec("self.workflow[0].view_error = 'waiting'")
self.assertTrue(
wait_for(self.wi, 'view_error', lambda v: v == "waiting", 30))
self.view.huescale = "log"
self.assertTrue(wait_for(self.wi, 'view_error', lambda v: v == "", 30))
from cytoflowgui.subset import CategorySubset
self.workflow.remote_exec("self.workflow[0].view_error = 'waiting'")
self.assertTrue(
wait_for(self.wi, 'view_error', lambda v: v == "waiting", 30))
self.view.xfacet = ""
self.view.yfacet = ""
self.view.subset_list.append(
CategorySubset(name="Well", values=['A', 'B']))
self.view.subset_list[0].selected = ['A']
self.assertTrue(wait_for(self.wi, 'view_error', lambda v: v == "", 30))
def testSubset(self):
from cytoflowgui.subset import CategorySubset
self.workflow.remote_exec("self.workflow[0].view_error = 'waiting'")
self.assertTrue(
wait_for(self.wi, 'view_error', lambda v: v == "waiting", 5))
self.view.subset_list.append(
CategorySubset(name="Well", values=['A', 'B']))
self.view.subset_list[0].selected = ['A']
self.assertTrue(wait_for(self.wi, 'view_error', lambda v: v == "", 5))
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 = BarChartPlugin()
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", 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):
ImportedDataTest.setUp(self)
self.workflow.remote_exec("self.workflow[0].view_error = 'waiting'")
self.wi = self.workflow.workflow[0]
self.assertTrue(wait_for(self.wi, 'view_error', lambda v: v == "waiting", 5))
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, 23124.058843387455),
(510.94519955277201, 23124.058843387455),
(1089.5215641232173, 3800.3424832180476),
(340.56382570202402, 801.98947404942271),
(65.42597937575897, 1119.3133482602157)]
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.workflow.remote_exec("self.workflow[-1].default_view.vertices = [(23.411982294776319, 5158.7027015021222), (102.22182270573683, 23124.058843387455), (510.94519955277201, 23124.058843387455), (1089.5215641232173, 3800.3424832180476), (340.56382570202402, 801.98947404942271), (65.42597937575897, 1119.3133482602157)]")
self.assertTrue(wait_for(wi, 'status', lambda v: v == 'valid', 15))
def setUp(self):
ImportedDataTest.setUp(self)
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"]))
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', 30))
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.wi_waitfor(stats_wi_2, 'status', 'valid')