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')
