def onRectangle(self, rectangle_geometry):
polygon_extent = utils.extentPolygon(rectangle_geometry)
# the current _selected_ layer in ArcMap
layer = utils.selectedLayer()
if layer is None:
return None
# store the results in memory, no need to bring spindles into this
output_feature = 'in_memory/primary_selection_points'
utils.intersectFeatures(layer.name, polygon_extent, output_feature)
# get the stats for our inviduals
indiv_stats = utils.selectIndividuals(output_feature, self.display)
"""
so we'd probably want to identify the specific columns of interest (haplotypes?),
perhaps using a drop-down menu, and then use the select tool to generate our areas of
interest, and shoot back out some summary statistics based on those observations.
"""
results = {
'indiv_stats': indiv_stats,
'output_feature': output_feature
}
# push results to a shared variable
config.primary_results = results
return results
def onRectangle(self, rectangle_geometry):
polygon_extent = utils.extentPolygon(rectangle_geometry)
# the current _selected_ layer in ArcMap
layer = utils.selectedLayer()
if layer is None:
return None
# store the results in memory, no need to bring spindles into this
output_feature = 'in_memory/primary_selection_points'
utils.intersectFeatures(layer.name, polygon_extent, output_feature)
# get the stats for our inviduals
indiv_stats = utils.selectIndividuals(output_feature, self.display)
"""
so we'd probably want to identify the specific columns of interest (haplotypes?),
perhaps using a drop-down menu, and then use the select tool to generate our areas of
interest, and shoot back out some summary statistics based on those observations.
"""
results = {'indiv_stats': indiv_stats, 'output_feature': output_feature}
# push results to a shared variable
config.primary_results = results
return results
def onRectangle(self, rectangle_geometry):
with open(config.log_path, 'a') as log:
polygon_extent = utils.extentPolygon(rectangle_geometry)
layer = utils.selectedLayer()
if layer is None:
return None
log.write("Compare encounters operating on layer {}\n".format(layer.name))
output_feature = 'in_memory/compare_selection_points'
utils.intersectFeatures(layer.name, polygon_extent, output_feature)
res2 = utils.selectIndividuals(output_feature, False)
# XXX now, get the results from the summarize encounters tool,
# and add these selection results back to the table
fields = arcpy.ListFields(layer.dataSource)
field_name = settings.population_field
try:
if field_name not in fields:
log.write("Adding {} to {}\n".format(field_name, layer.dataSource))
arcpy.AddField_management(layer.dataSource, field_name, 'TEXT')
if config.primary_results is None:
pythonaddins.MessageBox("Please make first selection before running"
" this tool", "requires primary selection")
return None
first_pop = config.primary_results['indiv_stats']['unique']
second_pop = res2['unique']
if len(first_pop) == 0:
pythonaddins.MessageBox("No results in primary selection.")
return None
if len(second_pop) == 0:
pythonaddins.MessageBox("No results in secondary selection.")
return None
log.write("Setting populations as {}, and {}\n".format(first_pop, second_pop))
with arcpy.da.UpdateCursor(layer, [settings.id_field, field_name]) as cur:
for row in cur:
id_field = row[0]
if id_field in first_pop and id_field in second_pop:
pop = 'both populations'
elif id_field in second_pop:
pop = 'second population only'
elif id_field in first_pop:
pop = 'first population only'
else:
pop = None
row[1] = pop
cur.updateRow(row)
except Exception as e:
msg = "Error adding {} column.".format(field_name)
title = "Compare Encounters: Selecting Populations"
f.write("Selecting populations generated Exception: %s\n" % e)
pythonaddins.MessageBox(msg, title)
return None
if self.display:
log.write("primary results: {}\n".format(config.primary_results))
if config.primary_results is not None:
res = config.primary_results['indiv_stats']
common_indiv = res['unique'].intersection(res2['unique'])
# compare the two sets of results
msg = ("First Set: {0} samples, "
"{1} unique individuals\n"
"Second Set: {2} samples, "
"{3} unique individuals\n\n"
"Common to both: {4}\n\n"
"Results saved to field \"{5}\"".format(
len(res['indiv']), len(res['unique']),
len(res2['indiv']), len(res2['unique']),
len(common_indiv)), field_name)
title = "Comparison Results"
pythonaddins.MessageBox(msg, title)
else:
pythonaddins.Messagebox("Please select first set", "Selection Missing")
else:
log.write("Not displaying output as display is set to {}".format(self.display))
def onRectangle(self, rectangle_geometry):
with open(config.log_path, 'a') as log:
polygon_extent = utils.extentPolygon(rectangle_geometry)
layer = utils.selectedLayer()
if layer is None:
return None
log.write("Compare encounters operating on layer {}\n".format(
layer.name))
output_feature = 'in_memory/compare_selection_points'
utils.intersectFeatures(layer.name, polygon_extent, output_feature)
res2 = utils.selectIndividuals(output_feature, False)
# XXX now, get the results from the summarize encounters tool,
# and add these selection results back to the table
fields = arcpy.ListFields(layer.dataSource)
field_name = settings.population_field
try:
if field_name not in fields:
log.write("Adding {} to {}\n".format(
field_name, layer.dataSource))
arcpy.AddField_management(layer.dataSource, field_name,
'TEXT')
if config.primary_results is None:
pythonaddins.MessageBox(
"Please make first selection before running"
" this tool", "requires primary selection")
return None
first_pop = config.primary_results['indiv_stats']['unique']
second_pop = res2['unique']
if len(first_pop) == 0:
pythonaddins.MessageBox("No results in primary selection.")
return None
if len(second_pop) == 0:
pythonaddins.MessageBox(
"No results in secondary selection.")
return None
log.write("Setting populations as {}, and {}\n".format(
first_pop, second_pop))
with arcpy.da.UpdateCursor(
layer, [settings.id_field, field_name]) as cur:
for row in cur:
id_field = row[0]
if id_field in first_pop and id_field in second_pop:
pop = 'both populations'
elif id_field in second_pop:
pop = 'second population only'
elif id_field in first_pop:
pop = 'first population only'
else:
pop = None
row[1] = pop
cur.updateRow(row)
except Exception as e:
msg = "Error adding {} column.".format(field_name)
title = "Compare Encounters: Selecting Populations"
f.write("Selecting populations generated Exception: %s\n" % e)
pythonaddins.MessageBox(msg, title)
return None
if self.display:
log.write("primary results: {}\n".format(
config.primary_results))
if config.primary_results is not None:
res = config.primary_results['indiv_stats']
common_indiv = res['unique'].intersection(res2['unique'])
# compare the two sets of results
msg = ("First Set: {0} samples, "
"{1} unique individuals\n"
"Second Set: {2} samples, "
"{3} unique individuals\n\n"
"Common to both: {4}\n\n"
"Results saved to field \"{5}\"".format(
len(res['indiv']), len(res['unique']),
len(res2['indiv']), len(res2['unique']),
len(common_indiv)), field_name)
title = "Comparison Results"
pythonaddins.MessageBox(msg, title)
else:
pythonaddins.Messagebox("Please select first set",
"Selection Missing")
else:
log.write(
"Not displaying output as display is set to {}".format(
self.display))