def testSubset(self): self.workflow.wi_sync(self.wi, 'view_error', 'waiting') from cytoflowgui.subset import CategorySubset, RangeSubset 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 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", 30)) 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 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 setUp(self): ImportedDataTest.setUp(self) plugin = ChannelStatisticPlugin() self.op = op = plugin.get_operation() op.name = "MeanByDox" op.channel = "Y2-A" op.statistic_name = "Geom.Mean" 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', 10))
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", 30)) 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) 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, 23124.0588433874530), (510.94519955277201, 23124.0588433874530), (1089.5215641232173, 3800.3424832180476), (340.56382570202402, 801.98947404942271), (65.42597937575897, 1119.3133482602157)]" ) self.assertTrue(wait_for(wi, 'status', lambda v: v == 'valid', 130))
def setUp(self): ImportedDataTest.setUp(self) plugin = ThresholdPlugin() self.op = op = plugin.get_operation() op.name = "Thresh" op.channel = "Y2-A" op.threshold = 1000 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 = 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')