Why is Clip_analysis giving ERROR 999999 using SHAPE@ geometry token as clip_features in arcpy.da.SearchCursor?

Question

In my file geodatabase (C:\polygeo\test.gdb) I have two feature classes:

• PointsFC which has 400 points arranged in a 20x20 grid
• FishnetFC which has four polygons arranged in a 2x2 grid - this has a field called Name that has values FC1, FC2, FC3 and FC4

When I run the script below I expect that the Clip tool will be taking the shape geometry as a token (SHAPE@) from each polygon in FishnetFC in turn and using it to clip out 100 points from PointsFC into a separate feature class called FC1, FC2, FC3 and FC4 in the current workspace (C:\polygeo\test.gdb).

import arcpy

inputFC = "C:/temp/test.gdb/PointsFC"
splitFC = "C:/temp/test.gdb/FishnetFC"
splitField = "Name"

arcpy.env.workspace = "C:/temp/test.gdb"
arcpy.env.overwriteOutput = True

with arcpy.da.SearchCursor(splitFC,[splitField,"SHAPE@"]) as cursor:
    for row in cursor:
        print "Clipping " + row[0]
        print str(row[1])
        arcpy.Clip_analysis(inputFC,row[1],row[0])
        print "Clip completed!"

print "Script finished!"

However, immediately after an uninstall/reinstall of ArcGIS 10.2.2 for Desktop (letting it install Python) I got the errors below from running it three times in IDLE:

Python 2.7.5 (default, May 15 2013, 22:43:36) [MSC v.1500 32 bit (Intel)] on win32
Type "copyright", "credits" or "license()" for more information.
>>> ================================ RESTART ================================
>>> 
Clipping FC1
<geoprocessing describe geometry object object at 0x026BFF20>

Traceback (most recent call last):
  File "C:\temp\test.py", line 22, in <module>
    arcpy.Clip_analysis(inputFC,row[1],row[0])
  File "C:\Program Files (x86)\ArcGIS\Desktop10.2\arcpy\arcpy\analysis.py", line 56, in Clip
    raise e
ExecuteError: ERROR 999999: Error executing function.
The table was not found. [FC1]
Failed to execute (Clip).

>>> ================================ RESTART ================================
>>> 
Clipping FC1
<geoprocessing describe geometry object object at 0x0278FF20>

Traceback (most recent call last):
  File "C:\temp\test.py", line 16, in <module>
    arcpy.Clip_analysis(inputFC,row[1],row[0])
  File "C:\Program Files (x86)\ArcGIS\Desktop10.2\arcpy\arcpy\analysis.py", line 56, in Clip
    raise e
ExecuteError: ERROR 999999: Error executing function.
Failed to execute (Clip).

>>> ================================ RESTART ================================
>>> 
Clipping FC1
<geoprocessing describe geometry object object at 0x0279FF20>

Traceback (most recent call last):
  File "C:\temp\test.py", line 14, in <module>
    arcpy.Clip_analysis(inputFC,row[1],row[0])
  File "C:\Program Files (x86)\ArcGIS\Desktop10.2\arcpy\arcpy\analysis.py", line 56, in Clip
    raise e
ExecuteError: ERROR 999999: Error executing function.
The table was not found. [FC1]
Failed to execute (Clip).

Does anyone know why? What confuses me is:

• On the first run, before which I made sure "C:/temp/test.gdb/FC1" did not exist, it complains that The table was not found. [FC1] and then leaves an empty point feature class called FC1 in the file geodatabase.
• For the second run, I left FC1 in place, and the error message changed to make no such mention.
• For the third run I deleted FC1 and the message reverted to include The table was not found. [FC1] so I think this should be giving me a hint about what is astray but I am not yet sure what.

---

Test which generates its own data

To try and get something easy for anyone to test I just enhanced the above script to generate its own test data, and then to perform the desired processing.

If anyone runs this using ArcGIS 10.2.2 for Desktop (like me) or any version that is at least 10.1:

import arcpy

inputFC = "C:/temp/test.gdb/TEMP_label"
splitFC = "C:/temp/test.gdb/FishnetFC"
splitField = "Name"

if arcpy.Exists("C:/temp/test.gdb"):
    arcpy.Delete_management("C:/temp/test.gdb")
arcpy.CreateFileGDB_management("C:/temp","test.gdb")

arcpy.CreateFishnet_management(out_feature_class="C:/temp/test.gdb/FishnetFC",
                               origin_coord="0 0",y_axis_coord="0 1",
                               cell_width="1",cell_height="1",
                               number_rows="2",number_columns="2",
                               corner_coord="#",labels="NO_LABELS",
                               template="#",geometry_type="POLYGON")
arcpy.AddField_management(in_table="C:/temp/test.gdb/FishnetFC",
                          field_name="Name",field_type="TEXT",
                          field_precision="#",field_scale="#",
                          field_length="10",field_alias="#",
                          field_is_nullable="NULLABLE",
                          field_is_required="NON_REQUIRED",field_domain="#")
arcpy.CalculateField_management(in_table="C:/temp/test.gdb/FishnetFC",
                                field="Name",
                                expression=""""FC" + str( !OID! )""",
                                expression_type="PYTHON_9.3",code_block="#")

arcpy.CreateFishnet_management(out_feature_class="C:/temp/test.gdb/TEMP",
                               origin_coord="0 0",y_axis_coord="0 1",
                               cell_width="0.1",cell_height="0.1",
                               number_rows="20",number_columns="20",
                               corner_coord="#",labels="LABELS",
                               template="#",geometry_type="POLYLINE")

arcpy.env.workspace = "C:/temp/test.gdb"
arcpy.env.overwriteOutput = True

with arcpy.da.SearchCursor(splitFC,[splitField,"SHAPE@"]) as cursor:
    for row in cursor:
        print "Clipping " + row[0]
        print str(row[1])
        name = row[0]
        geom = row[1]
        arcpy.Clip_analysis(inputFC,geom,name)
        print "Clip completed!"

print "Script finished!"

I would expect them to see (based on my results):

>>> ================================ RESTART ================================
>>> 
Clipping FC1
<geoprocessing describe geometry object object at 0x01DE7620>

Traceback (most recent call last):
  File "C:\temp\test.py", line 44, in <module>
    arcpy.Clip_analysis(inputFC,geom,name)
  File "C:\Program Files (x86)\ArcGIS\Desktop10.2\arcpy\arcpy\analysis.py", line 56, in Clip
    raise e
ExecuteError: ERROR 999999: Error executing function.
The table was not found. [FC1]
Failed to execute (Clip).

Answer 1

I can't explain why Clip is failing when you pass in the geometry. It happens for me as well.

I can offer this workaround, though. Persist that geometry out to in_memory (or to disk), then clip with it.

with arcpy.da.SearchCursor(splitFC, [splitField,"SHAPE@"]) as cursor:
   for row in cursor:
       name = row[0]
       geom = row[1]
       in_memory_feature = "in_memory\\" + name
       # Create temporary in-memory feature class
       arcpy.management.CopyFeatures(geom, in_memory_feature)
       # Perform clip
       arcpy.analysis.Clip(inputFC, in_memory_feature, name + "_clip")
       # Delete temporary in-memory feature class
       arcpy.management.Delete(in_memory_feature)

Answer 2

I'm getting the same error in my Arc 10.2 installation. I've encountered issues in the past when using geometry objects with geoprocessing tools, as you're doing with the geom object from your cursor and the Clip tool. It's just ironic since this is almost exactly the example in the Esri help page. One solution is to avoid using geometry objects by exporting the clipping features to a feature class (either on disk or in memory) as KHibma showed in his answer. I've come up with an alternative.

---

After doing some testing, it seems like tools don't like operating on geometry objects without spatial reference information. I redefined the spatial reference in the input objects to WGS84:

spatialRef = arcpy.SpatialReference(4326)
for file in [inputFC,splitFC]:
    arcpy.DefineProjection_management(file, spatialRef)

But even when the geometry objects being read by the searchCursor have a spatial reference, it still throws the error. But for some reason, if you create an entirely new geometry object in memory, everything runs fine:

with arcpy.da.SearchCursor(splitFC,[splitField,"SHAPE@"]) as cursor:
    for row in cursor:
        print "Clipping " + row[0]
        print str(row[1])
        name = row[0]
        geom = arcpy.Polygon(row[1].getPart(0),spatialRef) #New geometry object with SR
        arcpy.Clip_analysis(inputFC,geom,name)
        print "Clip completed!"