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 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 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 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): 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): WorkflowTest.setUp(self) plugin = ImportPlugin() op = plugin.get_operation() from cytoflow import Tube op.conditions = {"Dox" : "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" : 0.0, "Well" : 'A'}) tube2 = Tube(file = self.cwd + "/../../cytoflow/tests/data/Plate01/RFP_Well_A3.fcs", conditions = {"Dox" : 10.0, "Well" : 'A'}) tube3 = Tube(file = self.cwd + "/../../cytoflow/tests/data/Plate01/YFP_Well_A7.fcs", conditions = {"Dox" : 100.0, "Well" : 'A'}) tube4 = Tube(file = self.cwd + "/../../cytoflow/tests/data/Plate01/CFP_Well_B4.fcs", conditions = {"Dox" : 0.0, "Well" : 'B'}) tube5 = Tube(file = self.cwd + "/../../cytoflow/tests/data/Plate01/RFP_Well_A6.fcs", conditions = {"Dox" : 10.0, "Well" : 'B'}) tube6 = Tube(file = self.cwd + "/../../cytoflow/tests/data/Plate01/YFP_Well_C7.fcs", conditions = {"Dox" : 100.0, "Well" : 'B'}) op.tubes = [tube1, tube2, tube3, tube4, tube5, tube6] 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): 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')