Exercise 4#

Important

Please complete this exercise by the end of day on Friday, 2 December, 2022 (the day of next week’s work session).

To start this assignment, accept the GitHub Classroom assignment, and clone your own repository, e.g., in a CSC Notebook instance. Make sure you commit and push all changes you make (you can revisit instructions on how to use git and the jupyterlab git-plugin on the website of the Geo-Python course.

To preview the exercise without logging in, you can find the open course copy of the course’s GitHub repository at github.com/automating-gis-processes-2022/exercise-4. Don’t attempt to commit changes to that repository, but rather work with your personal GitHub Classroom copy (see above).

Hints#

Joining two data frames on different column names#

We have already joined data sets that share the same index, and also used spatial joins to merge geo-data frames depending on their geometric relationships.

For problem 1, it might be handy to be able to join two data sets using the values of two columns that have a different name. One good approach is to set the index of both data frames to refer to the same column:

import pandas

df1 = pandas.DataFrame({
    "id": [1, 2, 3],
    "other_column": ["a", "b", "c"]
})

df1
id other_column
0 1 a
1 2 b
2 3 c 
df2 = pandas.DataFrame({
    "id": [67, 68, 69],
    "other_other_column": ["x", "y", "z"],
    "df1_id": [1, 2, 3]
})
df2
id other_other_column df1_id
0 67 x 1
1 68 y 2
2 69 z 3 
joint_df = df1.set_index("id").join(df2.set_index("df1_id"))
joint_df
other_column id other_other_column
id
1 a 67 x
2 b 68 y
3 c 69 z

Renaming columns when joining data frames#

It is often necessary to rename columns when we join data frames that have duplicate column names. In the example below, both df1 and df2 have a column other_column; the join fails. An appropriate fix is to add a suffix to all columns of one or both of the data frames:

import pandas

df1 = pandas.DataFrame({
    "id": [1, 2, 3],
    "other_column": ["a", "b", "c"]
})

df1
id other_column
0 1 a
1 2 b
2 3 c 
df2 = pandas.DataFrame({
    "id": [67, 68, 69],
    "other_other_column": ["x", "y", "z"],
    "df1_id": [1, 2, 3]
})
df2
id other_other_column df1_id
0 67 x 1
1 68 y 2
2 69 z 3 
# Will fail, because duplicate column names exist:
joint_df = df1.join(df2)
joint_df

---------------------------------------------------------------------------
ValueError                                Traceback (most recent call last)
Cell In [6], line 2
      1 # Will fail, because duplicate column names exist:
----> 2 joint_df = df1.join(df2)
      3 joint_df

File ~/checkouts/readthedocs.org/user_builds/autogis-site/envs/2022/lib/python3.10/site-packages/pandas/core/frame.py:9966, in DataFrame.join(self, other, on, how, lsuffix, rsuffix, sort, validate)
   9803 def join(
   9804     self,
   9805     other: DataFrame | Series | list[DataFrame | Series],
   (...)
   9811     validate: str | None = None,
   9812 ) -> DataFrame:
   9813     """
   9814     Join columns of another DataFrame.
   9815 
   (...)
   9964     5  K1  A5   B1
   9965     """
-> 9966     return self._join_compat(
   9967         other,
   9968         on=on,
   9969         how=how,
   9970         lsuffix=lsuffix,
   9971         rsuffix=rsuffix,
   9972         sort=sort,
   9973         validate=validate,
   9974     )

File ~/checkouts/readthedocs.org/user_builds/autogis-site/envs/2022/lib/python3.10/site-packages/pandas/core/frame.py:10005, in DataFrame._join_compat(self, other, on, how, lsuffix, rsuffix, sort, validate)
   9995     if how == "cross":
   9996         return merge(
   9997             self,
   9998             other,
   (...)
  10003             validate=validate,
  10004         )
> 10005     return merge(
  10006         self,
  10007         other,
  10008         left_on=on,
  10009         how=how,
  10010         left_index=on is None,
  10011         right_index=True,
  10012         suffixes=(lsuffix, rsuffix),
  10013         sort=sort,
  10014         validate=validate,
  10015     )
  10016 else:
  10017     if on is not None:

File ~/checkouts/readthedocs.org/user_builds/autogis-site/envs/2022/lib/python3.10/site-packages/pandas/core/reshape/merge.py:124, in merge(left, right, how, on, left_on, right_on, left_index, right_index, sort, suffixes, copy, indicator, validate)
     93 @Substitution("\nleft : DataFrame or named Series")
     94 @Appender(_merge_doc, indents=0)
     95 def merge(
   (...)
    108     validate: str | None = None,
    109 ) -> DataFrame:
    110     op = _MergeOperation(
    111         left,
    112         right,
   (...)
    122         validate=validate,
    123     )
--> 124     return op.get_result(copy=copy)

File ~/checkouts/readthedocs.org/user_builds/autogis-site/envs/2022/lib/python3.10/site-packages/pandas/core/reshape/merge.py:775, in _MergeOperation.get_result(self, copy)
    771     self.left, self.right = self._indicator_pre_merge(self.left, self.right)
    773 join_index, left_indexer, right_indexer = self._get_join_info()
--> 775 result = self._reindex_and_concat(
    776     join_index, left_indexer, right_indexer, copy=copy
    777 )
    778 result = result.__finalize__(self, method=self._merge_type)
    780 if self.indicator:

File ~/checkouts/readthedocs.org/user_builds/autogis-site/envs/2022/lib/python3.10/site-packages/pandas/core/reshape/merge.py:729, in _MergeOperation._reindex_and_concat(self, join_index, left_indexer, right_indexer, copy)
    726 left = self.left[:]
    727 right = self.right[:]
--> 729 llabels, rlabels = _items_overlap_with_suffix(
    730     self.left._info_axis, self.right._info_axis, self.suffixes
    731 )
    733 if left_indexer is not None:
    734     # Pinning the index here (and in the right code just below) is not
    735     #  necessary, but makes the `.take` more performant if we have e.g.
    736     #  a MultiIndex for left.index.
    737     lmgr = left._mgr.reindex_indexer(
    738         join_index,
    739         left_indexer,
   (...)
    744         use_na_proxy=True,
    745     )

File ~/checkouts/readthedocs.org/user_builds/autogis-site/envs/2022/lib/python3.10/site-packages/pandas/core/reshape/merge.py:2458, in _items_overlap_with_suffix(left, right, suffixes)
   2455 lsuffix, rsuffix = suffixes
   2457 if not lsuffix and not rsuffix:
-> 2458     raise ValueError(f"columns overlap but no suffix specified: {to_rename}")
   2460 def renamer(x, suffix):
   2461     """
   2462     Rename the left and right indices.
   2463 
   (...)
   2474     x : renamed column name
   2475     """

ValueError: columns overlap but no suffix specified: Index(['id'], dtype='object')

# works: add a suffix to one of the data sets’ columns
joint_df = df1.join(df2.add_suffix("_df2"))
joint_df
id other_column id_df2 other_other_column_df2 df1_id_df2
0 1 a 67 x 1
1 2 b 68 y 2
2 3 c 69 z 3

Searching for files using a pattern#

In Lesson 2 we discussed how to use a file pattern to search for files, using pathlib.Path.glob().

To loop over all files ending in _s.shp inside DATA_DIRECTORY / "finland_topographic_database, use the following piece of code:

import pathlib
DATA_DIRECTORY = pathlib.Path().resolve() / "data"

for input_file in (DATA_DIRECTORY / "finland_topographic_database").glob("*_s.shp"):
    print(input_file.name)

k_L4132R_s.shp
m_L4132R_s.shp
l_L4132R_s.shp
j_L4132R_s.shp
s_L4132R_s.shp
n_L4132R_s.shp
r_L4132R_s.shp

This will come in handy for problem 2, when reading in all travel time data files. Be sure to revisit the explanation in Lesson 2.

Find the minimum value across multiple columns#

For problem 2, you have to find the smallest value across multiple columns: the shortest travel time to any of the eight shopping centres. For this, panda’s DataFrame.min() method can come in handy. It identifies the smallest value in each column or row (it accepts the same axis= parameter as apply()).

For instance, to find the smalles value for each row across the columns a, b, and c of the data frame below, use the following code:

import pandas

df = pandas.DataFrame(
    {
        "id": [1, 2, 3],
        "a": [27, 64, 12],
        "b": [13, 13, 13],
        "c": [34, 15, 1]
    }
)

df
id a b c
0 1 27 13 34
1 2 64 13 15
2 3 12 13 1 
# select which columns to compare, then call `.min()`
df[["a", "b", "c"]].min(axis=1)

0    13
1    13
2     1
dtype: int64

To find out which column had the smallest value for each row, use the near-identical method idxmin():

df[["a", "b", "c"]].idxmin(axis=1)

0    b
1    b
2    c
dtype: object

Of course, equivalent methods to find the greatest values exist: they are named pandas.DataFrame.max() and pandas.DataFrame.idxmax().