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I want to go through large CSV files and if there is missing data I want to remove that row completely, This is only row specific so if there is a cell that = 0 or has no value then I want to remove the entire row. I want this to happen for all the columns so if any column has a black cell it should delete the row, and return the corrected data in a corrected csv.
import csv
with open('data.csv', 'r') as csvfile:
csvreader = csv.reader(csvfile)
for row in csvreader:
print(row)
if not row[0]:
print("12")
This is what I found and tried but it doesnt not seem to be working and I dont have any ideas about how to aproach this problem, help please?
Thanks!
Due to the way in which CSV reader presents rows of data, you need to know how many columns there are in the original CSV file. For example, if the CSV file content looks like this:
1,2
3,
4
Then the lists return by iterating over the reader would look like this:
['1','2']
['3','']
['4']
As you can see, the third row only has one column whereas the first and second rows have 2 columns albeit that one is (effectively) empty.
This function allows you to either specify the number of columns (if you know them before hand) or allow the function to figure it out. If not specified then it is assumed that the number of columns is the greatest number of columns found in any row.
So...
import csv
DELIMITER = ','
def valid_column(col):
try:
return float(col) != 0
except ValueError:
pass
return len(col.strip()) > 0
def fix_csv(input_file, output_file, cols=0):
if cols == 0:
with open(input_file, newline='') as indata:
cols = max(len(row) for row in csv.reader(indata, delimiter=DELIMITER))
with open(input_file, newline='') as indata, open(output_file, 'w', newline='') as outdata:
writer = csv.writer(outdata, delimiter=DELIMITER)
for row in csv.reader(indata, delimiter=DELIMITER):
if len(row) == cols:
if all(valid_column(col) for col in row):
writer.writerow(row)
fix_csv('original.csv', 'fixed.csv')
maybe like this
import csv
with open('data.csv', 'r') as csvfile:
csvreader = csv.reader(csvfile)
data=list(csvreader)
data=[x for x in data if '' not in x and '0' not in x]
you can then rewrite the the csv file if you like
Instead of using csv, you should use Pandas module, something like this.
import pandas as pd
df = pd.read_csv('file.csv')
print(df)
index = 1 #index of the row that you want to remove
df = df.drop(index)
print(df)
df.to_csv('file.csv')
Analysis software I'm using outputs many groups of results in 1 csv file and separates the groups with 2 empty lines.
I would like to break the results in groups so that I can then analyse them separately.
I'm sure there is a built-in function in python (or one of it's libraries) that does this, I tried this piece of code that I found somewhere but it doesn't seem to work.
import csv
results = open('03_12_velocity_y.csv').read().split("\n\n")
# Feed first csv.reader
first_csv = csv.reader(results[0], delimiter=',')
# Feed second csv.reader
second_csv = csv.reader(results[1], delimiter=',')
Update:
The original code actually works, but my python skills are pretty limited and I did not implement it properly.
.split(\n\n\n) method does work but the csv.reader is an object and to get the data in a list (or something similar), it needs to iterate through all the rows and write them to the list.
I then used Pandas to remove the header and convert the scientific notated values to float. Code is bellow. Thanks everyone for help.
import csv
import pandas as pd
# Open the csv file, read it and split it when it encounters 2 empty lines (\n\n\n)
results = open('03_12_velocity_y.csv').read().split('\n\n\n')
# Create csv.reader objects that are used to iterate over rows in a csv file
# Define the output - create an empty multi-dimensional list
output1 = [[],[]]
# Iterate through the rows in the csv file and append the data to the empty list
# Feed first csv.reader
csv_reader1 = csv.reader(results[0].splitlines(), delimiter=',')
for row in csv_reader1:
output1.append(row)
df = pd.DataFrame(output1)
# remove first 7 rows of data (the start position of the slice is always included)
df = df.iloc[7:]
# Convert all data from string to float
df = df.astype(float)
If your row counts are inconsistent across groups, you'll need a little state machine to check when you're between groups and do something with the last group.
#!/usr/bin/env python3
import csv
def write_group(group, i):
with open(f"group_{i}.csv", "w", newline="") as out_f:
csv.writer(out_f).writerows(group)
with open("input.csv", newline="") as f:
reader = csv.reader(f)
group_i = 1
group = []
last_row = []
for row in reader:
if row == [] and last_row == [] and group != []:
write_group(group, group_i)
group = []
group_i += 1
continue
if row == []:
last_row = row
continue
group.append(row)
last_row = row
# flush remaining group
if group != []:
write_group(group, group_i)
I mocked up this sample CSV:
g1r1c1,g1r1c2,g1r1c3
g1r2c1,g1r2c2,g1r2c3
g1r3c1,g1r3c2,g1r3c3
g2r1c1,g2r1c2,g2r1c3
g2r2c1,g2r2c2,g2r2c3
g3r1c1,g3r1c2,g3r1c3
g3r2c1,g3r2c2,g3r2c3
g3r3c1,g3r3c2,g3r3c3
g3r4c1,g3r4c2,g3r4c3
g3r5c1,g3r5c2,g3r5c3
And when I run the program above I get three CSV files:
group_1.csv
g1r1c1,g1r1c2,g1r1c3
g1r2c1,g1r2c2,g1r2c3
g1r3c1,g1r3c2,g1r3c3
group_2.csv
g2r1c1,g2r1c2,g2r1c3
g2r2c1,g2r2c2,g2r2c3
group_3.csv
g3r1c1,g3r1c2,g3r1c3
g3r2c1,g3r2c2,g3r2c3
g3r3c1,g3r3c2,g3r3c3
g3r4c1,g3r4c2,g3r4c3
g3r5c1,g3r5c2,g3r5c3
If your row counts are consistent, you can do this with fairly vanilla Python or using the Pandas library.
Vanilla Python
Define your group size and the size of the break (in "rows") between groups.
Loop over all the rows adding each row to a group accumulator.
When the group accumulator reaches the pre-defined group size, do something with it, reset the accumulator, and then skip break-size rows.
Here, I'm writing each group to its own numbered file:
import csv
group_sz = 5
break_sz = 2
def write_group(group, i):
with open(f"group_{i}.csv", "w", newline="") as f_out:
csv.writer(f_out).writerows(group)
with open("input.csv", newline="") as f_in:
reader = csv.reader(f_in)
group_i = 1
group = []
for row in reader:
group.append(row)
if len(group) == group_sz:
write_group(group, group_i)
group_i += 1
group = []
for _ in range(break_sz):
try:
next(reader)
except StopIteration: # gracefully ignore an expected StopIteration (at the end of the file)
break
group_1.csv
g1r1c1,g1r1c2,g1r1c3
g1r2c1,g1r2c2,g1r2c3
g1r3c1,g1r3c2,g1r3c3
g1r4c1,g1r4c2,g1r4c3
g1r5c1,g1r5c2,g1r5c3
With Pandas
I'm new to Pandas, and learning this as I go, but it looks like Pandas will automatically trim blank rows/records from a chunk of data^1.
With that in mind, all you need to do is specify the size of your group, and tell Pandas to read your CSV file in "iterator mode", where you can ask for a chunk (your group size) of records at a time:
import pandas as pd
group_sz = 5
with pd.read_csv("input.csv", header=None, iterator=True) as reader:
i = 1
while True:
try:
df = reader.get_chunk(group_sz)
except StopIteration:
break
df.to_csv(f"group_{i}.csv")
i += 1
Pandas add an "ID" column and default header when it writes out the CSV:
group_1.csv
,0,1,2
0,g1r1c1,g1r1c2,g1r1c3
1,g1r2c1,g1r2c2,g1r2c3
2,g1r3c1,g1r3c2,g1r3c3
3,g1r4c1,g1r4c2,g1r4c3
4,g1r5c1,g1r5c2,g1r5c3
TRY this out with your output:
import pandas as pd
# csv file name to be read in
in_csv = 'input.csv'
# get the number of lines of the csv file to be read
number_lines = sum(1 for row in (open(in_csv)))
# size of rows of data to write to the csv,
# you can change the row size according to your need
rowsize = 500
# start looping through data writing it to a new file for each set
for i in range(1,number_lines,rowsize):
df = pd.read_csv(in_csv,
header=None,
nrows = rowsize,#number of rows to read at each loop
skiprows = i)#skip rows that have been read
#csv to write data to a new file with indexed name. input_1.csv etc.
out_csv = 'input' + str(i) + '.csv'
df.to_csv(out_csv,
index=False,
header=False,
mode='a', #append data to csv file
)
I updated the question with the last details that answer my question.
So I'm trying to combine column values from one csv to another while saving it into a final csv file. But I want to iterate through all the rows adding the column values of each row to each row of the original csv.
In other words say csv1 has 3 rows.
Row 1: Frog,Rat,Duck
Row 2: Cat,Dog,Cow
Row 3: Moose,Fox,Zebra
And I want to combine 2 more column values from csv2 to each of those rows.
Row 1: Chicken,Pig
Row 2:
Row 3: Bear,Boar
So csv3 would end up looking like.
Row 1: Frog,Rat,Duck,Chicken,Pig
Row 2: Moose,Fox,Zebra,Bear,Boar
But at the same time if there's a row in csv2 that has no values at all I don't want it to copy the row from csv1. In other words that row will not exist at all in the final csv file. I prefer not to use pandas as I have just been using the csv module thus far throughout my code but any method is appreciated.
So far I have come across this method which works if there's only one single row. But when there's more than that it just adds random lines and appends the values all over the place. And it combines both of the columns into one string while adding an extra blank line at the end of the csv for some odd reason.
import csv
f1 = open ("2.csv","r", encoding='utf-8')
with open("3.csv","w", encoding='utf-8', newline='') as f:
writer = csv.writer(f)
with open("1.csv","r", encoding='utf-8') as csvfile:
reader = csv.reader(csvfile, delimiter=",")
for row in reader:
row[6] = f1.readline()
writer.writerow(row)
f1.close()
Using the same example csvs above the results given are.
Frog,Rat,Duck,Chicken,Pig
Cat,Dog,Cow
Moose,Fox,Zebra,Bear,Boar
You can zip together the two files and then iterate through each row. Then you can concatenate the two lists and write the result to a file.
To check if there is an empty row we can compare the set of the row to the set of an empty string.
import csv
new_csv_data = []
EMPTY_ROW = set([""])
with open("1.csv", "r", newline="") as first_file, open("2.csv", "r", newline="") as second_file, open("3.csv", "w", newline="") as out_file:
first_file_reader = csv.reader(first_file)
second_file_reader = csv.reader(second_file)
out_file_writer = csv.writer(out_file)
# The iterator will stop when the shortest file is finished
for row_1, row_2 in zip(first_file_reader, second_file_reader):
# Check if the second row is empty, skipping if it is
if not row_2 or set(row_2) == EMPTY_ROW:
continue
out_file_writer.writerow(row_1 + row_2)
I have a csv file where I need to delete the second and the third row and 3rd to 18th column. I was able to do get it to work in two steps, which produced an interim file. I am thinking that there must be a better and more compact way to do this. Any suggestions would be really appreciated.
Also, if I want to remove multiple ranges of columns, how do I specify in this code. For example, if I want to remove columns 25 to 29, in addition to columns 3 to 18 already specified, how would I add to the code? Thanks
remove_from = 2
remove_to = 17
with open('file_a.csv', 'rb') as infile, open('interim.csv', 'wb') as outfile:
reader = csv.reader(infile)
writer = csv.writer(outfile)
for row in reader:
del row[remove_from : remove_to]
writer.writerow(row)
with open('interim.csv', 'rb') as infile, open('file_b.csv', 'wb') as outfile:
reader = csv.reader(infile)
writer = csv.writer(outfile)
writer.writerow(next(reader))
reader.next()
reader.next()
for row in reader:
writer.writerow(row)
Here is a pandas approach:
Step 1, creating a sample dataframe
import pandas as pd
# Create sample CSV-file (100x100)
df = pd.DataFrame(np.arange(10000).reshape(100,100))
df.to_csv('test.csv', index=False)
Step 2, doing the magic
import pandas as pd
import numpy as np
# Read first row to determine size of columns
size = pd.read_csv('test.csv',nrows=0).shape[1]
#want to remove columns 25 to 29, in addition to columns 3 to 18 already specified,
# Ok so let's create an array with the length of dataframe deleting the ranges
ranges = np.r_[3:19,25:30]
ar = np.delete(np.arange(size),ranges)
# Now let's read the dataframe
# let us also skip rows 2 and 3
df = pd.read_csv('test.csv', skiprows=[2,3], usecols=ar)
# And output
dt.to_csv('output.csv', index=False)
And the proof:
Here's a sample csv file;
out_gate,uless_col,in_gate,n_con
p,x,x,1
p,x,y,1
p,x,z,1
a_a,u,b,1
a_a,s,b,3
a_b,e,a,2
a_b,l,c,4
a_c,e,a,5
a_c,s,b,5
a_c,s,b,3
a_c,c,a,4
a_d,o,c,2
a_d,l,c,3
a_d,m,b,2
p,y,x,1
p,y,y,1
p,y,z,3
I want to remove the useless columns (2nd column) and useless rows (first three and last three rows) and create a new csv file and then save this new one. and How can I deal with the csv file that has more than 10 useless columns and useless rows?
(assuming useless rows are located only on the top or the bottom lines not scattered in the middle)
(and I am also assuming all the rows we want to use has its first element name starting with 'a_')
Can I get solution without using numpys or pandas as well? thanks!
Assuming that you have one or more unwanted columns and the wanted rows start with "a_".
import csv
with open('filename.csv') as infile:
reader = csv.reader(infile)
header = next(reader)
data = list(reader)
useless = set(['uless_col', 'n_con']) # Let's say there are 2 useless columns
mask, new_header = zip(*[(i,name) for i,name in enumerate(header)
if name not in useless])
#(0,2) - column mask
#('out_gate', 'in_gate') - new column headers
new_data = [[row[i] for i in mask] for row in data] # Remove unwanted columns
new_data = [row for row in new_data if row[0].startswith("a_")] # Remove unwanted rows
with open('filename.csv', 'w') as outfile:
writer = csv.writer(outfile)
writer.writerow(new_header)
writer.writerows(new_data)
You can try this:
import csv
data = list(csv.reader(open('filename.csv')))
header = [data[0][0]]+data[0][2:]
final_data = [[i[0]]+i[2:] for i in data[1:]][3:-3]
with open('filename.csv', 'w') as f:
write = csv.writer(f)
write.writerows([header]+final_data)
Output:
out_gate,in_gate,n_con
a,b,1
a,b,3
b,a,2
b,c,4
c,a,5
c,b,5
c,b,3
c,a,4
d,c,2
d,c,3
d,b,2
Below solution uses Pandas.
As the pandas dataframe drop function suggests, you can do the following:
import pandas as pd
df = pd.read_csv("csv_name.csv")
df.drop(columns=['ulesscol'])
Above code is considering dropping columns, you can drop rows by index as:
df.drop([0, 1])
Alternatively, don't read in the column in the first place:
df = pd.read_csv("csv_name.csv",
usecols=["out_gate", "in_gate", "n_con"])