[GRASS-dev] Write array to (point) attribute table
Paulo van Breugel
p.vanbreugel at gmail.com
Thu Oct 1 08:34:26 PDT 2015
Hi Michel,
Thanks! I think I got the suggestions by Anna, Pietro and Moritz
working, but this certainly looks like an handy function to have at
hand. One possible disadvantage if using this in a script to be shared
with others is that it would add an dependency on pandas, wouldn't it?
Cheers,
Paulo
On 01-10-15 10:01, Michel Wortmann wrote:
> Hi Paulo,
> I had the same problem some time ago. I am using pandas for a lot of
> things and discovered the quickest way to append a column to a vector
> table is using pandas' .to_sql dataframe method. Here is my full
> function for it:
>
> import pandas as pa
> dataframe = pa.DataFrame( ... )
> def appendColumns(vecttbl,dataframe,join=None,layer=1):
> '''Upload a DataFrame (Series should be first converted into a sql compliant datafram)
> to a grass vector table. Join is a valid column in vecttbl or if None take categories.
> Always joins on df.index, which is not uploaded.'''
> # get sqlite.db info
> db = grass.vector_db(vecttbl)[layer]
> con = sqlite3.connect(db['database'])
> # decide join indeces
> itbl = {False:db['key'],True:join}[join!=None]
> # make series to dataframe
> dataframe.to_sql('pandas_temp',con,if_exists='replace',index_label='ix') # index label?
> # join columns to vecttbl
> grass.run_command('v.db.join',map=vecttbl,column=itbl,
> other_table='pandas_temp',other_column='ix',
> subset_columns=','.join(map(str,dataframe.columns)))
> # remove temp table
> cur = con.cursor()
> cur.execute('DROP TABLE IF EXISTS pandas_temp')
> con.commit(); con.close()
> return
>
> The dataframe.to_sql line is essentially all you need, the rest of the
> function is just prepping.
> Hope it helps,
> Michel
>
>
> On 10/01/2015 12:05 AM, Paulo van Breugel wrote:
>>
>>
>> On 30-09-15 17:52, Paulo van Breugel wrote:
>>>
>>>
>>> On 30-09-15 17:47, Anna Petrášová wrote:
>>>>
>>>>
>>>> On Wed, Sep 30, 2015 at 11:20 AM, Paulo van Breugel
>>>> <p.vanbreugel at gmail.com> wrote:
>>>>
>>>>
>>>>
>>>> On 30-09-15 16:18, Anna Petrášová wrote:
>>>>>
>>>>>
>>>>> On Wed, Sep 30, 2015 at 9:27 AM, Paulo van Breugel
>>>>> <p.vanbreugel at gmail.com <mailto:p.vanbreugel at gmail.com>> wrote:
>>>>>
>>>>>
>>>>>
>>>>> On Wed, Sep 30, 2015 at 11:53 AM, Pietro
>>>>> <peter.zamb at gmail.com> wrote:
>>>>>
>>>>> On Wed, Sep 30, 2015 at 9:51 AM, Paulo van Breugel
>>>>> <p.vanbreugel at gmail.com> wrote:
>>>>> >
>>>>> >
>>>>> > On Wed, Sep 30, 2015 at 2:02 AM, Anna Petrášová
>>>>> <kratochanna at gmail.com>
>>>>> > wrote:
>>>>> >>
>>>>> >>
>>>>> >>
>>>>> >> On Tue, Sep 29, 2015 at 6:09 PM, Paulo van Breugel
>>>>> >> <p.vanbreugel at gmail.com> wrote:
>>>>> >>>
>>>>> >>> This must be a very basic question, but I can't
>>>>> find an easy/direct way
>>>>> >>> to do this. In python, if I have an array with
>>>>> values with a length equal to
>>>>> >>> the number of rows in an attribute table of a
>>>>> (point) vector layer, how can
>>>>> >>> I write those values to a new column in that
>>>>> attribute table. I can of
>>>>> >>> course first create the column, but than how to
>>>>> update that column with the
>>>>> >>> values in the array?
>>>>> >>
>>>>> >>
>>>>> >> it should be pretty easy to do with pygrass,
>>>>> unfortunately there is no
>>>>> >> example on assigning attributes in the official
>>>>> documentation [1], but it
>>>>> >> should be pretty easy, something like that (not
>>>>> tested):
>>>>> >>
>>>>> >> with VectorTopo('myvector', mode='w') as vectormap:
>>>>> >> for feature in vectormap:
>>>>> >> feature.attrs['mycolumn'] = value
>>>>> >>
>>>>> >>
>>>>> > Thanks, but that seems to write the vector back
>>>>> without attribute table
>>>>>
>>>>> You have to save the changes in the database out from
>>>>> your cycle, with:
>>>>>
>>>>> vectormap.table.conn.commit()
>>>>>
>>>>>
>>>>> Thanks Pietro. I am, however, not sure I understand (I
>>>>> tried to use it, but thanks to my limited experience in
>>>>> Python / pygrass not much luck). Just to be more specific,
>>>>> I am trying to create a script that divides points in
>>>>> training and test groups, similar to v.kcv, but with
>>>>> points clustered in space. E.g.,
>>>>>
>>>>> # Create vector
>>>>> grass.run_command("v.random", output="testB", npoints=10,
>>>>> overwrite=True)
>>>>> grass.run_command("v.db.addtable", map="testB", columns="X
>>>>> DOUBLE PRECISION,Y DOUBLE PRECISION,GR INTEGER")
>>>>> grass.run_command("v.to.db", map="test", option="coor",
>>>>> columns="X,Y")
>>>>>
>>>>> # Create groups
>>>>> vectmap = 'test'
>>>>> cvals = array(grass.vector_db_select(vectmap, layer =
>>>>> int(1), columns = 'X,Y')['values'].values()).astype(np.float)
>>>>> centroids,_ = kmeans(cvals,2)
>>>>> idx,_ = vq(cvals,centroids)
>>>>>
>>>>> # write results to tabel
>>>>> Now I would like to write idx to the column 'GR' in the
>>>>> attribute table of 'test'.
>>>>>
>>>>> p.s. I am first creating the XY columns now, but is there
>>>>> a function to get the coordinates (cvals) in pygrass directly?
>>>>>
>>>>>
>>>>> I don't fully understand the example,
>>>>
>>>> Thanks for the quick response. I basically have a list with
>>>> values (idx in the example above) which I like to add as a
>>>> column to the attribute table of an existing vector (point
>>>> layer). The length of idx is equal to the number of rows in the
>>>> attribute table. The solution of Anna seems like an elegant
>>>> solution (and easier and more flexible than other solutions I
>>>> tried using e.g., sqlite3). However, as I wrote, I end up with
>>>> a vector without attribute table. You wrote that I "have to
>>>> save the changes in the database out from your cycle, with:
>>>> vectormap.table.conn.commit()". I am, however, not sure what
>>>> you mean with 'out from your cycle' or how to implement that.
>>>>
>>>>
>>>> probably after the for cycle ends you would call this
>>>> 'vectormap.table.conn.commit()', if it doesn't works, try to put it
>>>> in the cycle (I am not sure what is supposed to work).
>>>
>>> I did try both, with no luck so-far. I'll give it another try
>>> though, perhaps I did something else wrong.
>>
>> Tried out again, but after running the code below, I end up with an
>> empty vector layer (no points and no attribute table). Same if I put
>> the vectormap.table.conn.commit() in the for cycle.
>>
>> import grass.script as grass
>> from grass.pygrass.vector import VectorTopo
>> grass.run_command("v.random", output="testB", npoints=10, overwrite=True)
>> grass.run_command("v.db.addtable", map="testB", columns="GR INTEGER")
>> with VectorTopo('testB', mode='w') as vectormap:
>> for feature in vectormap:
>> feature.attrs['GR'] = 9
>> vectormap.table.conn.commit()
>>
>>>>
>>>>> but yes, you can get coordinates:
>>>>>
>>>>> with VectorTopo('myvector', mode='w') as vectormap:
>>>>> for feature in vectormap:
>>>>> print feature.x
>>>>> print feature.y
>>>>
>>>> Great, thanks. I did not find this in the manual. If it is not
>>>> there, perhaps it would be something worth including? I would
>>>> not mind providing a text, but I am not sure what would be the
>>>> best way to do that.
>>>>
>>>>
>>>> Technically, it's in the manual:
>>>> https://grass.osgeo.org/grass70/manuals/libpython/pygrass_vector.html#geometry-classes
>>>>
>>>> but we are lacking more examples of often used constructions. Some
>>>> other examples are available in the recent workshop we did:
>>>>
>>>> https://github.com/wenzeslaus/python-grass-addon/blob/master/02_pygrass_library.ipynb
>>>
>>> Thanks, I will have a look at it.
>>>>
>>>>
>>>>>
>>>>>
>>>>> Pietro
>>>>>
>>>>>
>>>>>
>>>>
>>>>
>>>
>>
>>
>>
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