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How to combine h5 data numpy arrays based on date in filename?

I have hundreds of .h5 files with dates in their filename (e.g ...20221017...). For each file, I have extracted some parameters into a numpy array of the format
[[param_1a, param_2a...param_5a],
...
[param_1x, param_2x,...param_5x]]
which represents data of interest. I want to group the data by month, so instead of having (e.g) 30 arrays for one month, I have 1 array which represents the average of the 30 arrays. How can I do this?
This is the code I have so far, filename represents a txt file of file names.
def combine_months(filename):
fin = open(filename, 'r')
next_name = fin.readline()
while (next_name != ""):
year = next_name[6:10]
month = next_name[11:13]
date = month+'\\'+year
#not sure where to go from here
fin.close()
An example of what I hope to achieve is that say array_1, array_2, array_3 are numpy arrays representing data from different h5 files with the same month in the date of their filename.
array_1 = [[ 1 4 10]
[ 2 5 11]
[3 6 12]]
array_2 = [[ 1 2 5]
[ 2 2 3]
[ 3 6 12]]
array_3 = [[ 2 4 10]
[ 3 2 3]
[ 4 6 12]]
I want the result to look like:
2022_04_data = [[1,3,7.5]
[2, 2, 6.5]
[3,4,7.5]
[4,6,12]]
Note that the first number of each row represents an ID, so I need to group those data together based on the first number as well.

Ok, here is the beginning of an answer. (I suspect you may have more questions as you work thru the details.)
There are several ways to get the filenames. You could put them in a file, but it's easier (and better IMHO) to use the glob.iglob() function. There are 2 examples below that show how to: 1) open each file, 2) read the data from the data dataset into an array, and 3) append the array to a list. The first example has the file names in a list. The second uses the glob.iglob() function to get the filenames. (You could also use glob.glob() to create a list of names.)
Method 1: read filenames from list
import h5py
arr_list = []
for h5file in ['20221001.h5', '20221002.h5', '20221003.h5']:
with h5py.File(h5file,'r') as h5f:
arr = h5f['data'][()]
#print(arr)
arr_list.append(arr)
Method 2: use glob.iglob() to get files using wildcard names
import h5py
from glob import iglob
arr_list = []
for h5file in iglob('202210*.h5'):
with h5py.File(h5file,'r') as h5f:
print(h5f.keys()) # to get the dataset names from the keys
arr = h5f['data'][()]
#print(arr)
arr_list.append(arr)
After you have read the datasets into arrays, you iterate over the list, do your calculations and create a new array from the results. Code below shows how to get the shape and dtype.
for arr in arr_list:
# do something with the data based on column 0 value
print(arr.shape, arr.dtype)
Code below shows a way to sum rows with matching column 0 values. Without more details it's hard to show exactly how to do this. It reads all column 0 values into a sorted list, then uses to size count and sum arrays, then as a index to the proper row.
# first create a list from column 0 values, then sort
row_value_list = []
for arr in arr_list:
col_vals = arr[:,0]
for val in col_vals:
if val not in row_value_list:
row_value_list.append(val)
# Sort list of column IDs
row_value_list.sort()
# get length index list to create cnt and sum arrays
a0 = len(row_value_list)
# get shape and dtype from 1st array, assume constant for all
a1 = arr_list[0].shape[1]
dt = arr_list[0].dtype
arr_cnt = np.zeros(shape=(a0,a1),dtype=dt)
arr_cnt[:,0] = row_value_list
arr_sum = np.zeros(shape=(a0,a1),dtype=dt)
arr_sum[:,0] = row_value_list
for arr in arr_list:
for row in arr:
idx = row_value_list.index(row[0])
arr_cnt[idx,1:] += 1
arr_sum[idx,1:] += row[1:]
print('Count Array\n',arr_cnt)
print('Sum Array\n',arr_sum)
arr_ave = arr_sum/arr_cnt
arr_ave[:,0] = row_value_list
print('Average Array\n',arr_ave)
Here is an alternate way to create row_value_list from a set. It's simpler because sets don't retain duplicate values, so you don't have to check for existing values when adding them to row_value_set.
# first create a set from column 0 values, then create a sorted list
row_value_set = set()
for arr in arr_list:
col_vals = set(arr[:,0])
row_value_set = row_value_set.union(col_vals)
row_value_list = sorted(row_value_set)

This is a new, updated answer that addresses the comment/request about calculating the median. (It also calculates the mean, and can be easily extended to calculate other statistics from the masked array.)
As noted in my comment on Nov 4 2022, "starting from my first answer quickly got complicated and hard to follow". This process is similar but different from the first answer. It uses glob to get a list of filenames (instead of iglob). Instead of loading the H5 datasets into a list of arrays, it loads all of the data into a single array (data is "stacked" on the 0-axis.). I don't think this increases the memory footprint. However, memory could be a problem if you load a lot of very large datasets for analysis.
Summary of the procedure:
Use glob.glob() to load filenames to a list based on a wildcard
Allocate an array to hold all the data (arr_all) based on the # of
files and size of 1 dataset.
Loop thru all H5 files, loading data to arr_all
Create a sorted list of unique group IDs (column 0 values)
Allocate arrays to hold mean/median (arr_mean and arr_median) based on the # of unique row IDs and # of columns in arr_all.
Loop over values in ID list, then:
a. Create masked array (mask) where column 0 value = loop value
b. Broadcast mask to match arr_all shape then apply to create ma_arr_all
c. Loop over columns of ma_arr_all, compress to get unmasked values, then calculate mean and median and save.
Code below:
import h5py
from glob import glob
import numpy as np
# use glob.glob() to get list of files using wildcard names
file_list = glob('202210*.h5')
with h5py.File(file_list[0],'r') as h5f:
a0, a1 = h5f['data'].shape
# allocate array to hold values from all datasets
arr_all = np.zeros(shape=(len(file_list)*a0,a1), dtype=h5f['data'].dtype)
start, stop = 0, a0
for i, h5file in enumerate(file_list):
with h5py.File(h5file,'r') as h5f:
arr_all[start:stop,:] = h5f['data'][()]
start += a0
stop += a0
# Create a set from column 0 values, and use to create a sorted list
row_value_list = sorted(set(arr_all[:,0]))
arr_mean = np.zeros(shape=(len(row_value_list),arr_all.shape[1]))
arr_median = np.zeros(shape=(len(row_value_list),arr_all.shape[1]))
col_0 = arr_all[:,0:1]
for i, row_val in enumerate(row_value_list):
row_mask = np.where(col_0==row_val, False, True ) # True mask value ignores data.
all_mask= np.broadcast_to(row_mask, arr_all.shape)
ma_arr_all = np.ma.masked_array(arr_all, mask=all_mask)
for j in range(ma_arr_all.shape[1]):
masked_col = ma_arr_all[:,j:j+1].compressed()
arr_mean[i:i+1,j:j+1] = np.mean(masked_col)
arr_median[i:i+1,j:j+1] = np.median(masked_col)
print('Mean values:\n',arr_mean)
print('Median values:\n',arr_median)
Added Nov 22, 2022:
Method above uses np.broadcast_to() introduced in NumPy 1.10. Here is an alternate method for prior versions. (Replaces the entire for i, row_val loop.) It should be more memory efficient. I haven't profiled to verify, but arrays all_mask and ma_arr_all are not created.
for i, row_val in enumerate(row_value_list):
row_mask = np.where(col_0==row_val, False, True ) # True mask value ignores data.
for j in range(arr_all.shape[1]):
masked_col = np.ma.masked_array(arr_all[:,j:j+1], mask=row_mask).compressed()
arr_mean[i:i+1,j:j+1] = np.mean(masked_col)
arr_median[i:i+1,j:j+1] = np.median(masked_col)
I ran with values provided by OP. Output is provided below and is the same for both methods:
Mean values:
[[ 1. 3. 7.5 ]
[ 2. 3.66666667 8. ]
[ 3. 4.66666667 9. ]
[ 4. 6. 12. ]]
Median values:
[[ 1. 3. 7.5]
[ 2. 4. 10. ]
[ 3. 6. 12. ]
[ 4. 6. 12. ]]

How to split a column into many columns where the name of this columns change

I defined a data frame into a "function" where the name of each column in the dataframes changes continuously so I can't specify the name of this column and then split it to many columns. For example, I can't say df ['name'] and then split it into many columns. The number of columns and rows of this dataframes is not constant. I need to split any column contains more than one item to many components (columns).
For example:
This is one of the dataframes which I have:
name/one name/three
(192.26949,) (435.54,436.65,87.3,5432)
(189.4033245,) (45.51,56.612, 54253.543, 54.321)
(184.4593252,) (45.58,56.6412,654.876,765.66543)
I want to convert it to:
name/one name/three1 name/three2 name/three3 name/three4
192.26949 435.54 436.65 87.3 5432
189.4033245 45.51 56.612 54253.543 54.321
184.4593252 45.58 56.6412 654.876 765.66543

Solution if all data are tuples in all rows and all columns use concat with DataFrame constructor and DataFrame.add_prefix:
df = pd.concat([pd.DataFrame(df[c].tolist()).add_prefix(c) for c in df.columns], axis=1)
print (df)
name/one0 name/three0 name/three1 name/three2 name/three3
0 192.269490 435.54 436.6500 87.300 5432.00000
1 189.403324 45.51 56.6120 54253.543 54.32100
2 184.459325 45.58 56.6412 654.876 765.66543
If possible string repr of tuples:
import ast
L = [pd.DataFrame([ast.literal_eval(y) for y in df[c]]).add_prefix(c) for c in df.columns]
df = pd.concat(L, axis=1)
print (df)
name/one0 name/three0 name/three1 name/three2 name/three3
0 192.269490 435.54 436.6500 87.300 5432.00000
1 189.403324 45.51 56.6120 54253.543 54.32100
2 184.459325 45.58 56.6412 654.876 765.66543

How to compare columns of two dataframes and have consequences when they match in Python Pandas

I am trying to have Python Pandas compare two dataframes with each other. In dataframe 1, i have two columns (AC-Cat and Origin). I am trying to compare the AC-Cat column with the inputs of Dataframe 2. If a match is found between one of the columns of Dataframe 2 and the value of dataframe 1 being studied, i want Pandas to copy the header of the column of Dataframe 2 in which the match is found to a new column in Dataframe 1.
DF1:
f = {'AC-Cat': pd.Series(['B737', 'A320', 'MD11']),
'Origin': pd.Series(['AJD', 'JFK', 'LRO'])}
Flight_df = pd.DataFrame(f)
DF2:
w = {'CAT-C': pd.Series(['DC85', 'IL76', 'MD11', 'TU22', 'TU95']),
'CAT-D': pd.Series(['A320', 'A321', 'AN12', 'B736', 'B737'])}
WCat_df = pd.DataFrame(w)
I imported pandas as pd and numpy as np and tried to define a function to compare these columns.
def get_wake_cat(AC_cat):
try:
Wcat = [WCat_df.columns.values[0]][WCat_df.iloc[:,1]==AC_cat].values[0]
except:
Wcat = np.NAN
return Wcat
Flight_df.loc[:,'CAT'] = Flight_df.loc[:,'AC-Cat'].apply(lambda CT: get_wake_cat(CT))
However, the function does not result in the desired outputs. For example: Take the B737 AC-Cat value. I want Python Pandas to then find this value in DF2 in the column CAT-D and copy this header to the new column of DF 1. This does not happen. Can someone help me find out why my code is not giving the desired results?

Not pretty but I think I got it working. Part of the error was that the function did not have WCat_df. I also changed the indexing into two steps:
def get_wake_cat(AC_cat, WCat_df):
try:
d=WCat_df[WCat_df.columns.values][WCat_df.iloc[:]==AC_cat]
Wcat=d.columns[(d==AC_cat).any()][0]
except:
Wcat = np.NAN
return Wcat
Then you need to change your next line to:
Flight_df.loc[:,'CAT'] = Flight_df.loc[:,'AC-Cat'].apply(lambda CT: get_wake_cat(CT,WCat_df ))
AC-Cat Origin CAT
0 B737 AJD CAT-D
1 A320 JFK CAT-D
2 MD11 LRO CAT-C
Hope that solves the problem

This will give you 2 new columns with the name\s of the match\s found:
Flight_df['CAT1'] = Flight_df['AC-Cat'].map(lambda x: 'CAT-C' if x in list(WCat_df['CAT-C']) else '')
Flight_df['CAT2'] = Flight_df['AC-Cat'].map(lambda x: 'CAT-D' if x in list(WCat_df['CAT-D']) else '')
Flight_df.loc[Flight_df['CAT1'] == '', 'CAT1'] = Flight_df['CAT2']
Flight_df.loc[Flight_df['CAT1'] == Flight_df['CAT2'], 'CAT2'] = ''

IUC, you can do a stack and merge:
final=(Flight_df.merge(WCat_df.stack().reset_index(1,name='AC-Cat'),on='AC-Cat',how='left')
.rename(columns={'level_1':'New'}))
print(final)
Or with melt:
final=Flight_df.merge(WCat_df.melt(var_name='New',value_name='AC-Cat'),
on='AC-Cat',how='left')
AC-Cat Origin New
0 B737 AJD CAT-D
1 A320 JFK CAT-D
2 MD11 LRO CAT-C

How to calculate the mean and standard deviation of multiple dataframes at one go?

I've several hundreds of pandas dataframes and And the number of rows are not exactly the same in all the dataframes like some have 600 but other have 540 only.
So what i want to do is like, i have two samples of exactly the same numbers of dataframes and i want to read all the dataframes(around 2000) from both the samples. So that's how thee data looks like and i can read the files like this:
5113.440 1 0.25846 0.10166 27.96867 0.94852 -0.25846 268.29305 5113.434129
5074.760 3 0.68155 0.16566 120.18771 3.02654 -0.68155 101.02457 5074.745627
5083.340 2 0.74771 0.13267 105.59355 2.15700 -0.74771 157.52406 5083.337081
5088.150 1 0.28689 0.12986 39.65747 2.43339 -0.28689 164.40787 5088.141849
5090.780 1 0.61464 0.14479 94.72901 2.78712 -0.61464 132.25865 5090.773443
#first Sample
path_to_files = '/home/Desktop/computed_2d_blaze/'
lst = []
for filen in [x for x in os.listdir(path_to_files) if '.ares' in x]:
df = pd.read_table(path_to_files+filen, skiprows=0, usecols=(0,1,2,3,4,8),names=['wave','num','stlines','fwhm','EWs','MeasredWave'],delimiter=r'\s+')
df = df.sort_values('stlines', ascending=False)
df = df.drop_duplicates('wave')
df = df.reset_index(drop=True)
lst.append(df)
#second sample
path_to_files1 = '/home/Desktop/computed_1d/'
lst1 = []
for filen in [x for x in os.listdir(path_to_files1) if '.ares' in x]:
df1 = pd.read_table(path_to_files1+filen, skiprows=0, usecols=(0,1,2,3,4,8),names=['wave','num','stlines','fwhm','EWs','MeasredWave'],delimiter=r'\s+')
df1 = df1.sort_values('stlines', ascending=False)
df1 = df1.drop_duplicates('wave')
df1 = df1.reset_index(drop=True)
lst1.append(df1)
Now the data is stored in lists and as the number of rows in all the dataframes are not same so i cant subtract them directly.
So how can i subtract them correctly?? And after that i want to take average(mean) of the residual to make a dataframe?

You shouldn't use apply. Just use Boolean making:
mask = df['waves'].between(lower_outlier, upper_outlier)
df[mask].plot(x='waves', y='stlines')

One solution that comes into mind is writing a function that finds outliers based on upper and lower bounds and then slices the data frames based on outliers index e.g.
df1 = pd.DataFrame({'wave': [1, 2, 3, 4, 5]})
df2 = pd.DataFrame({'stlines': [0.1, 0.2, 0.3, 0.4, 0.5]})
def outlier(value, upper, lower):
"""
Find outliers based on upper and lower bound
"""
# Check if input value is within bounds
in_bounds = (value <= upper) and (value >= lower)
return in_bounds
# Function finds outliers in wave column of DF1
outlier_index = df1.wave.apply(lambda x: outlier(x, 4, 1))
# Return DF2 without values at outlier index
df2[outlier_index]
# Return DF1 without values at outlier index
df1[outlier_index]

Values in Pandas dataframe is mixed and shifted

Values in Pandas dataframe is mixed and shifted.But each column has its own characteristics for values in it. How can I rearrange values in their own position?
'floor_no' have to contain values with ' / ' substring in it.
'room_count' is maximum 2 values digit long.
sq_m_count' have to contain ' m²' substring in it.
'price_sq' have to contain ' USD/m²' in it.
'bs_state' have to contain one of 'Have' or 'Do not have' values.
Adding part of pandas dataframe.

Consider the following approach:
In [90]: dfs = []
In [91]: url = 'https://ru.bina.az/items/565674'
In [92]: dfs.append(pd.read_html(url)[0].set_index(0).T)
In [93]: url = 'https://ru.bina.az/items/551883'
In [94]: dfs.append(pd.read_html(url)[0].set_index(0).T)
In [95]: df = pd.concat(dfs, ignore_index=True)
In [96]: df
Out[96]:
0 Категория Площадь Количество комнат Купчая
0 Дом / Вилла 376 м² 6 есть
1 Дом / Вилла 605 м² 6 нет

I figured out solution that is bit "+18 and perverty"
I wrote a loop that looks if each of these columns contain some sting that identifies columnt that it belongs to and copies this value to new column. Then i simply subsituted new with old one.
I did this with each of 'mixed' columns. This code filled my needs and fixed all problem. I understand how 'perverted' code is and will write a function that is much shorter and professional.
for index in bina_az_df.itertuples():
bina_az_df.loc[bina_az_df['bs_state'].str.contains(" m²|sot"),'new_sq_m_count'] = bina_az_df['bs_state']
bina_az_df.loc[bina_az_df['sq_m_count'].str.contains(" m²|sot"),'new_sq_m_count'] = bina_az_df['sq_m_count']
bina_az_df.loc[bina_az_df['floor_no'].str.contains(" m²|sot"),'new_sq_m_count'] = bina_az_df['floor_no']
bina_az_df.loc[bina_az_df['price_sq'].str.contains(" m²|sot"),'new_sq_m_count'] = bina_az_df['price_sq']
bina_az_df.loc[bina_az_df['room_count'].str.contains(" m²|sot"),'new_sq_m_count'] = bina_az_df['room_count']
bina_az_df['sq_m_count'] = bina_az_df['new_sq_m_count'] # Substitutes
del bina_az_df['new_sq_m_count'] # deletes unnecesary temp column