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I've been working on a script which essentially reads in a large amount of point and polygon data and generates frequency values for a featureclass of 2.5 acre hexes covering California. I have found it necessary to write my own version of the frequency tool, as ESRI's default tool has been crashing ArcMap on an irregular basis, and this script needs to be reliable and predictable. To do this I have been using python dictionaries to store values that are read in from the input datasets. The dictionaries are 2 dimensional (each key contains another dictionary within it) and get quite extensive, as there are 60000+ keys with 1-28 secondary keys. Writing the dictionaries isn't the problem, however, those get written reasonably quickly.

My problem is when the dictionaries are done being constructed, running my makeshift frequency tool takes a long time. Here's the code and a short example of the dictionary entries, I'll explain a bit more below:

There are two dictionaries I read from, here's an example of 'otherSourceDict'. hexDict is handled a little differently (it uses two letter codes (AA, AB, etc...) instead of taxon names like 'Amphibian'), but basically stores the same information:

{13456: {'Amphibian': 2, 'Bird': 5, 'Mammal': 10, 'Plant': 20}, 43156: {'Fish': 1, 'Plant': 4}}

The primary keys (13456 and 43156) represent hex feature unique IDs. The secondary keys (Amphibian, Mammal...) contain the number of taxon observations that are in that hex.

My frequency code:

#Build a list of important correlated values for reference later
taxaList = [['RAR2_AMPH', 'AA', 'Amphibian', 'R2_NRM_A'],
            ['RAR2_BIRD', 'AB', 'Bird', 'R2_NRM_B'],
            ['RAR2_FISH', 'AF', 'Fish', 'R2_NRM_F'],
            ['RAR2_MAMM', 'AM', 'Mammal', 'R2_NRM_M'],
            ['RAR2_REPT', 'AR', 'Reptile', 'R2_NRM_R'],
            ['RAR2_PLNT', 'P', 'Plant', 'R2_NRM_P']]
#Add fields for taxa value by hex
sendmsg("     Adding fields...")
fieldList = gp.listfields(inRare)
for taxa in range(len(taxaList)):
    if not taxaList[taxa][0] in fieldList:
        gp.addfield_management(inRare, taxaList[taxa][0], "SHORT")
cur = gp.updatecursor(inRare)
row = cur.next()
sendmsg("     Writing dictionaries to hexs")
while row:
    #Count for user visualization of process completion
    if c%10000 == 0:
        sendmsg("          Starting record number " + str(c) + "...")
    #For each taxa, calculate the frequency and populate the corresponding field.
    for taxa in range(len(taxaList)):
        if str(int(row.HEX25_ID)) in hexDict.keys():
            #Search the CNDDB dictionary and count how many of each taxa per hex
            for elmcode in hexDict[str(int(row.HEX25_ID))].keys():
                #If dealing with taxa other than plants
                if elmcode != "ECO_SECT" and taxaList[taxa][1] != "P":
                    if elmcode[:2] == taxaList[taxa][1]:
                #If dealing with plants
                elif elmcode != "ECO_SECT" and taxaList[taxa][1] == "P":
                    if elmcode[0] == "P" or elmcode[0] == "N":
        if str(int(row.HEX25_ID)) in otherSourceDict.keys():
            #Search the other source dictionary and count how many of each taxa per hex
            for otherTaxa in otherSourceDict[str(int(row.HEX25_ID))].keys():
                if otherTaxa == taxaList[taxa][2]:
        #Populate the total number of each taxa per hex to the rare species hex features
        row.setValue(taxaList[taxa][0], val)
    row = cur.next()

del row, cur

So right now, I have it so that when it goes to populate the hex features, it loops through each row 5 times, one for each field, then runs the frequency calculation for the specified taxon, and populates the field. There are roughly 60000 rows that it does this for.

Does anyone have any suggestions or alternative methods for populating the hex features that could speed up the process? The script performs several operations, this by far takes the most time (about 25 minutes) and I would like to get it to be as quick as possible.

Thanks for your help and suggestions!

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perhaps creating a function that takes in the an integer of how many division processes. Then you could divide the table into say 10 recordsets and process the recordssets all together at about the same time. I also recently saw on the help.arcgis.com site showing how to actually spawn multiprocessing using python multiprocessing module. –  Justin Oct 24 '12 at 15:30
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2 Answers

up vote 3 down vote accepted

I think there may be unavoidable cursor transaction overhead to slow you down unless there is a way to update a large batch of rows at once. Comment out "cur.updaterow(row)" and run it again... is there a difference?

The secondary slow down in your case is a lot of unnecessary copying. dict.keys() copies values and you have many. Better to do "if k in dict" and "for k in dict" which compares your value k to the dict's keys.

Can you also avoid all the str(int(foo)) expressions? If foo is already a string representation of an int, you can save many (millions?) of calls.

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A couple thoughts on this: 1.) if I remove cur.updaterow(row), I believe that none of my records will retain the values I assign them once my cursor moves on to the next row. 2.) As far as the str(int(foo)) thing goes, I have to keep it this way, as when it pulls in foo all by itself it pulls it as a float value with a decimal (for some reason). I suppose I could truncate the last two values, but I'm not sure if that would improve much. I'll check out your suggestion to drop the .keys() and report back. Thanks –  egdetti Oct 24 '12 at 16:04
I only suggested you comment out the update for a speed test. Of course it's not going to update your database without that call. –  sgillies Oct 24 '12 at 16:21
It's been a while since I used ESRI products but I do remember how slow cursor updates were. Just a thought: can necessary calculations be processed while building the dictionary by calling appropriate functions? At one point I remember converting a list to a shapefile using open source due to crashes. Not sure if this is a credible alternative since I'm kind of new to GIS scripting. –  geomajor56 Oct 24 '12 at 17:52
I tested out removing .keys() and the results shocked me. My processing speed has improved significantly - down to 23 minutes from 46. A coworker has suggested that I look into C# for further improving process speeds, but for staying within Python, this is a very helpful tip. Thanks. –  egdetti Oct 25 '12 at 18:59
I'd bet lunch that 19 of the remaining 23 is cursor overhead. I don't see how C# will help unless it gives you access to fast bulk updates that you don't have from ArcPy. –  sgillies Oct 26 '12 at 14:45
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Two thoughts are:

  1. If Frequency is giving you problems you could try Summary Statistics with a Case Field to do the same thing
  2. Search cursors were relatively slow at 10.0 but at 10.1 arcpy.da (Data Access) provides improved cursor support (including performance).
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