Develop Reference

list index out of range in calculation of nodal distance

I am working on a small task in which I have to find the distance between two nodes. Each node has X and Y coordinates which can be seen below.
node_number X_coordinate Y_coordinate
0 0 1 0
1 1 1 1
2 2 1 2
3 3 1 3
4 4 0 3
5 5 0 4
6 6 1 4
7 7 2 4
8 8 3 4
9 9 4 4
10 10 4 3
11 11 3 3
12 12 2 3
13 13 2 2
14 14 2 1
15 15 2 0
For the purpose I mentioned above, I wrote below code,
X1_coordinate = df['X_coordinate'].tolist()
Y1_coordinate = df['Y_coordinate'].tolist()
node_number1 = df['node_number'].tolist()
nodal_dist = []
i = 0
for i in range(len(node_number1)):
dist = math.sqrt((X1_coordinate[i+1] - X1_coordinate[i])**2 + (Y1_coordinate[i+1] - Y1_coordinate[i])**2)
nodal_dist.append(dist)
I got the error
list index out of range
Kindly let me know what I am doing wrong and what should I change to get the answer.

Indexing starts at zero, so the last element in the list has an index that is one less than the number of elements in that list. But the len() function gives you the number of elements in the list (in other words, it starts counting at 1), so you want the range of your loop to be len(node_number1) - 1 to avoid an -off-by-one error.

The problems should been in this line
dist = math.sqrt((X1_coordinate[i+1] - X1_coordinate[i])**2 + (Y1_coordinate[i+1] - Y1_coordinate[i])**2)
the X1_coordinate[i+1] and the ] Y1_coordinate[i+1]] go out of range on the last number call.

Finding contiguous, non-unique slices in Pandas series without iterating

I'm trying to parse a logfile of our manufacturing process. Most of the time the process is run automatically but occasionally, the engineer needs to switch into manual mode to make some changes and then switches back to automatic control by the reactor software. When set to manual mode the logfile records the step as being "MAN.OP." instead of a number. Below is a representative example.
steps = [1,2,2,'MAN.OP.','MAN.OP.',2,2,3,3,'MAN.OP.','MAN.OP.',4,4]
ser_orig = pd.Series(steps)
which results in
0 1
1 2
2 2
3 MAN.OP.
4 MAN.OP.
5 2
6 2
7 3
8 3
9 MAN.OP.
10 MAN.OP.
11 4
12 4
dtype: object
I need to detect the 'MAN.OP.' and make them distinct from each other. In this example, the two regions with values == 2 should be one region after detecting the manual mode section like this:
0 1
1 2
2 2
3 Manual_Mode_0
4 Manual_Mode_0
5 2
6 2
7 3
8 3
9 Manual_Mode_1
10 Manual_Mode_1
11 4
12 4
dtype: object
I have code that iterates over this series and produces the correct result when the series is passed to my object. The setter is:
#step_series.setter
def step_series(self, ss):
"""
On assignment, give the manual mode steps a unique name. Leave
the steps done on recipe the same.
"""
manual_mode = "MAN.OP."
new_manual_mode_text = "Manual_Mode_{}"
counter = 0
continuous = False
for i in ss.index:
if continuous and ss.at[i] != manual_mode:
continuous = False
counter += 1
elif not continuous and ss.at[i] == manual_mode:
continuous = True
ss.at[i] = new_manual_mode_text.format(str(counter))
elif continuous and ss.at[i] == manual_mode:
ss.at[i] = new_manual_mode_text.format(str(counter))
self._step_series = ss
but this iterates over the entire dataframe and is the slowest part of my code other than reading the logfile over the network.
How can I detect these non-unique sections and rename them uniquely without iterating over the entire series? The series is a column selection from a larger dataframe so adding extra columns is fine if needed.
For the completed answer I ended up with:
#step_series.setter
def step_series(self, ss):
pd.options.mode.chained_assignment = None
manual_mode = "MAN.OP."
new_manual_mode_text = "Manual_Mode_{}"
newManOp = (ss=='MAN.OP.') & (ss != ss.shift())
ss[ss == 'MAN.OP.'] = 'Manual_Mode_' + (newManOp.cumsum()-1).astype(str)
self._step_series = ss

Here's one way:
steps = [1,2,2,'MAN.OP.','MAN.OP.',2,2,3,3,'MAN.OP.','MAN.OP.',4,4]
steps = pd.Series(steps)
newManOp = (steps=='MAN.OP.') & (steps != steps.shift())
steps[steps=='MAN.OP.'] += seq.cumsum().astype(str)
>>> steps
0 1
1 2
2 2
3 MAN.OP.1
4 MAN.OP.1
5 2
6 2
7 3
8 3
9 MAN.OP.2
10 MAN.OP.2
11 4
12 4
dtype: object
To get the exact format you listed (starting from zero instead of one, and changing from "MAN.OP." to "Manual_mode_"), just tweak the last line:
steps[steps=='MAN.OP.'] = 'Manual_Mode_' + (seq.cumsum()-1).astype(str)
>>> steps
0 1
1 2
2 2
3 Manual_Mode_0
4 Manual_Mode_0
5 2
6 2
7 3
8 3
9 Manual_Mode_1
10 Manual_Mode_1
11 4
12 4
dtype: object
There a pandas enhancement request for contiguous groupby, which would make this type of task simpler.

There is s function in matplotlib that takes a boolean array and returns a list of (start, end) pairs. Each pair represents a contiguous region where the input is True.
import matplotlib.mlab as mlab
regions = mlab.contiguous_regions(ser_orig == manual_mode)
for i, (start, end) in enumerate(regions):
ser_orig[start:end] = new_manual_mode_text.format(i)
ser_orig
0 1
1 2
2 2
3 Manual_Mode_0
4 Manual_Mode_0
5 2
6 2
7 3
8 3
9 Manual_Mode_1
10 Manual_Mode_1
11 4
12 4
dtype: object

Divide part of a dataframe by another while keeping columns that are not being divided

I have two data frames as below:
Sample_name C14-Cer C16-Cer C18-Cer C18:1-Cer C20-Cer
0 1 1 0.161456 0.033139 0.991840 2.111023 0.846197
1 1 10 0.636140 1.024235 36.333741 16.074662 3.142135
2 1 13 0.605840 0.034337 2.085061 2.125908 0.069698
3 1 14 0.038481 0.152382 4.608259 4.960007 0.162162
4 1 5 0.035628 0.087637 1.397457 0.768467 0.052605
5 1 6 0.114375 0.020196 0.220193 7.662065 0.077727
Sample_name C14-Cer C16-Cer C18-Cer C18:1-Cer C20-Cer
0 1 1 0.305224 0.542488 66.428382 73.615079 10.342252
1 1 10 0.814696 1.246165 73.802644 58.064363 11.179206
2 1 13 0.556437 0.517383 50.555948 51.913547 9.412299
3 1 14 0.314058 1.148754 56.165767 61.261950 9.142128
4 1 5 0.499129 0.460813 40.182454 41.770906 8.263437
5 1 6 0.300203 0.784065 47.359506 52.841821 9.833513
I want to divide the numerical values in the selected cells of the first by the second and I am using the following code:
df1_int.loc[:,'C14-Cer':].div(df2.loc[:,'C14-Cer':])
However, this way I lose the information from the column "Sample_name".
C14-Cer C16-Cer C18-Cer C18:1-Cer C20-Cer
0 0.528977 0.061088 0.014931 0.028677 0.081819
1 0.780831 0.821909 0.492309 0.276842 0.281070
2 1.088785 0.066367 0.041243 0.040951 0.007405
3 0.122529 0.132650 0.082047 0.080964 0.017738
4 0.071381 0.190178 0.034778 0.018397 0.006366
5 0.380993 0.025759 0.004649 0.145000 0.007904
How can I perform the division while keeping the column "Sample_name" in the resulting dataframe?

You can selectively overwrite using loc, the same way that you're already performing the division:
df1_int.loc[:,'C14-Cer':] = df1_int.loc[:,'C14-Cer':].div(df2.loc[:,'C14-Cer':])
This preserves the sample_name col:
In [12]:
df.loc[:,'C14-Cer':] = df.loc[:,'C14-Cer':].div(df1.loc[:,'C14-Cer':])
df
Out[12]:
Sample_name C14-Cer C16-Cer C18-Cer C18:1-Cer C20-Cer
index
0 1 1 0.528975 0.061087 0.014931 0.028677 0.081819
1 1 10 0.780831 0.821910 0.492309 0.276842 0.281070
2 1 13 1.088785 0.066367 0.041243 0.040951 0.007405
3 1 14 0.122528 0.132650 0.082047 0.080964 0.017738
4 1 5 0.071380 0.190179 0.034778 0.018397 0.006366
5 1 6 0.380992 0.025758 0.004649 0.145000 0.007904

Guessing Indentation of text file with python

I am working with a program that generates a specific file format, that I have to read and modify with python scripts. This file is is supposed to be tab delimited, but I haven't been able to recognize the tab character. Any good way to read this kind of file, and generate a new one in the same formatting?
1. Base Year Data for Calibration
1.1 Observed Data per Internal Zone
Sector Zone ExogProd InducedPro ExogDemand Price ValueAdded Attractor
1 1 5000 0 0 14409.8204 0 1
1 2 800 0 0 12628.4625 0 1
1 3 1100 0 0 12676.3341 0 1
2 1 0 3393.2241 0 13944.0613 0 1
2 2 0 732.1119 0 12340.4575 0 1
2 3 0 974.6630 0 12132.7666 0 1
3 1 0 4491.8722 0 2701.8266 0 1
3 2 0 12755.9657 0 2445.0556 0 1
3 3 0 4752.1604 0 2671.2305 0 1
4 1 0 1790.7874 0 3858.0189 0 1
4 2 0 3076.6366 0 3337.8784 0 1
4 3 0 11132.5806 0 3728.1412 0 1
5 1 0 69.5126 0 250000 250000 1
5 2 0 109.5081 0 120000 120000 1
5 3 0 124.2133 0 180000 180000 1
The problem is that when I read this with python with line.split('\t'), I end with just the whole line.

As others have pointed out in the comments, this appears to be just a space separated file with a variable number of spaces between cells. If that is the case, you can extract the cells from a particular row like this:
cells = line.split()
As for regenerating it, you'll need to pad the various columns to different widths. One way would be with code like this:
widths = [12,9,11,11,11,11,11,11]
paddedCells = [string.rjust(cell,widths[i]) for i,cell in enumerate(cells)]
line = ''.join(paddedCells)

actually I am using
%12d %8d %10.2f %10.2f %10.2f %10.2f %10.2f %10.1f\n
The problem seems to be how the file are generated. I am pretty sure is not tab-delimited files.

Pythonic way of copying values in an array with a complex rule

If the value in column a is 1 then the value of b is copied in column c until a is -1.
In the example below, a is 1 in row 2 and -1 in row 5. Then the second value in column b (13) is copied in column c from row 2 to 5.
row a b c
1 0 12 0
2 1 13 13
3 0 15 13
4 0 2 13
5 -1 19 13
6 0 34 0
7 0 11 0
8 1 23 23
9 0 14 23
10 -1 9 23
11 0 18 0
12 0 19 0
I've done this with a for loop, but there must be a more elegant way to do this manipulating series (I'm using pandas, numpy). All your help is greatly appreciated.

Here's a solution that does use a for loop but is pretty succinct while still being understandable.
I'm assuming you have the data stored in table, with a as table[:,0] and that a always appears as (1, -1)*, with 0 interspersed.
starts = table[:,0] == 1
ends = table[:,0] == -1
for start, end in zip(starts.nonzero()[0], ends.nonzero()[0]):
table[start:end+1,2] = table[start,1]
I bet there's some fancy way to get rid of that loop, but I'd also bet that it's harder to tell what's going on.
I agree with everyone else that if you post what you currently have it'd help to go from there.