I am trying to figure out a way to write an if statement based on a couple criteria. I have a large CSV file that I have cleaned and already organized. There are a couple things I need to do:
I first need a way that will check to see if the machine is "on" for more than 3 rows. If that is true then I need to get its corredsponding pressure for that cycle and find the average of it. For example, in the df aboce, in rows 14-19 the machine is on for more than 3 rows so then I need to get the average pressure across all instances in this period.
This data contains 40,000 rows, so I will then need this to cycle through the entire sheet to keep track of the total number of times the machine is on, and each corresponding average pressure.
import pandas as pd
import numpy as np
header_list = ['Time']
df = pd.read_csv('S8-1.csv' , skiprows=6 , names = header_list)
#splits the data into proper columns
df[['Date/Time','Pressure']] = df.Time.str.split(",,", expand=True)
#deletes orginal messy column
df.pop('Time')
#convert Pressure from object to numeric
df['Pressure'] = pd.to_numeric(df['Pressure'], errors = 'coerce')
#converts to a time
df['Date/Time'] = pd.to_datetime(df['Date/Time'], format = '%m/%d/%y %H:%M:%S.%f' , errors = 'coerce')
df['Moving Average'] = df['Pressure'].rolling(window=5).mean()
df['Rolling Average Center']= df['Pressure'].rolling(window=5, center=True).mean()
df['Machine On/Off'] = ['1' if x >= 115 else '0' for x in df['Rolling Average Center'] ]
arr = df['Machine On/Off']
def find_runs(x):
x = np.asanyarray(x)
if x.ndim !=1:
raise Valueerror('Only 1D array supported')
n = x.shape[0]
if n == 0:
return np.array([]), np.array([]), np.array([])
else:
loc_run_start = np.empty(n, dtype=bool)
loc_run_start[0] = True
np.not_equal(x[:-1], x[1:], out=loc_run_start[1:])
run_starts = np.nonzero(loc_run_start)[0]
# find run values
run_values = x[loc_run_start]
# find run lengths
run_lengths = np.diff(np.append(run_starts, n))
return run_values, run_starts, run_lengths
run = find_runs(arr)
df.iloc[_start:run_length]['whatever column']
Suggested first step: make new column with ones and zeros... 1 for on, 0 for off.
df['newcolumnname'] = 0
df['newcolumnname'][df['machine on/off'] == 'on'] = 1
Grab that column as a numpy array:
arr = df['newcolumnname'].to_numpy()
Then using the following code credit: https://gist.github.com/alimanfoo/c5977e87111abe8127453b21204c1065
import numpy as np
def find_runs(x):
"""Find runs of consecutive items in an array."""
# ensure array
x = np.asanyarray(x)
if x.ndim != 1:
raise ValueError('only 1D array supported')
n = x.shape[0]
# handle empty array
if n == 0:
return np.array([]), np.array([]), np.array([])
else:
# find run starts
loc_run_start = np.empty(n, dtype=bool)
loc_run_start[0] = True
np.not_equal(x[:-1], x[1:], out=loc_run_start[1:])
run_starts = np.nonzero(loc_run_start)[0]
# find run values
run_values = x[loc_run_start]
# find run lengths
run_lengths = np.diff(np.append(run_starts, n))
return run_values, run_starts, run_lengths
get the "runs"...should only have zeros and ones.
run_values, run_starts, run_lengths = find_runs(arr)
print(run_values) #just to see what order they are in
print(run_starts.shape)#get an idea of the shapes
print(run_lengths.shape)
_ix = run_values.tolist().index(1)
To get data from your pandas,
for _start, _run_length in zip(run_starts[_ix], run_lengths[_ix]):
tmp_df = df.iloc[_start:_start+_run_length]
#do what you want
print(tmp_df)
break #remove this...I just don't know how big your data is
You're correct when you are thinking "this answer does not run". But it should give you enough to get going and solve your problem.
Incomplete question gets an incomplete response.
TODO: make your machine on/off to be integer...not sure if it is absolutely needed, but if it's a numerical numpy array then there are more options available to you.
df['Machine On/Off'] = [1 if x >= 115 else 0 for x in df['Rolling Average Center'] ]
Related
I am calculating correlations and the data frame I have needs to be filtered.
I am looking to remove the rows under the current row from the data frame that are above or under by X amount starting with the first row and looping through the dataframe all the way until the last row.
example:
df['y'] has the values 50,51,52,53,54,55,70,71,72,73,74,75
if X = 10 it would start at 50 and see 51,52,53,54,55 as within that 10+- range and delete the rows. 70 would stay as it is not within that range and the same test would start again at 70 where 71,72,73,74,75 and respective rows would be deleted
the filter if X=10 would thus leave us with the rows including 50,75 for df.
It would leave me with a clean dataframe that deletes the instances that are linked to the first instance of what is essentially the same observed period. I tried coding a loop to do that but I am left with the wrong result and desperate at this point. Hopefully someone can correct the mistake or point me in the right direction.
df6['index'] = df6.index
df6.sort_values('index')
boom = len(dataframe1.index)/3
#Taking initial comparison values from first row
c = df6.iloc[0]['index']
#Including first row in result
filters = [True]
#Skipping first row in comparisons
for index, row in df6.iloc[1:].iterrows():
if c-boom <= row['index'] <= c+boom:
filters.append(False)
else:
filters.append(True)
# Updating values to compare based on latest accepted row
c = row['index']
df2 = df6.loc[filters].sort_values('correlation').drop('index', 1)
df2
OUTPUT BEFORE
OUTPUT AFTER
IIUC, your main issue is to filter consecutive values within a threshold.
You can use a custom function for that that acts on a Series (=column) to return the list of valid indices:
def consecutive(s, threshold = 10):
prev = float('-inf')
idx = []
for i, val in s.iteritems():
if val-prev > threshold:
idx.append(i)
prev = val
return idx
Example of use:
import pandas as pd
df = pd.DataFrame({'y': [50,51,52,53,54,55,70,71,72,73,74,75]})
df2 = df.loc[consecutive(df['y'])]
Output:
y
0 50
6 70
variant
If you prefer the function to return a boolean indexer, here is a varient:
def consecutive(s, threshold = 10):
prev = float('-inf')
idx = [False]*len(s)
for i, val in s.iteritems():
if val-prev > threshold:
idx[i] = True
prev = val
return idx
My current code functions and produces a graph if there is only 1 sensor, i.e. if col2, and col3 are deleted in the example data provided below, leaving one column.
import pandas as pd
import numpy as np
import matplotlib.pyplot as plt
d = {'col1': [-2587.944231, -1897.324231,-2510.304231,-2203.814231,-2105.734231,-2446.964231,-2963.904231,-2177.254231, 2796.354231,-2085.304231], 'col2': [-3764.468462,-3723.608462,-3750.168462,-3694.998462,-3991.268462,-3972.878462,3676.608462,-3827.808462,-3629.618462,-1841.758462,], 'col3': [-166.1357692,-35.36576923, 321.4157692,108.9257692,-123.2257692, -10.84576923, -100.7457692, 89.27423077, -211.0857692, 101.5342308]}
df = pd.DataFrame(data=d)
sensors = 3
window_size = 5
dfn = df.rolling(window_size).corr(pairwise = True)
index = df.index #index of values in the data frame.
rows = len(index) #len(index) returns number of rows in the data.
sensors = 3
baseline_num = [0]*(rows) #baseline numerator, by default zero
baseline = [0]*(rows) #initialize baseline value
baseline = DataFrame(baseline)
baseline_num = DataFrame(baseline_num)
v = [None]*(rows) # Initialize an empty array v[] equal to amount of rows in .csv file
s = [None]*(rows) #Initialize another empty array for the slope values for detecting when there is an exposure
d = [0]*(rows)
sensors_on = True #Is the sensor detecting something (True) or not (False).
off_count = 0
off_require = 8 # how many offs until baseline is updated
sensitivity = 1000
for i in range(0, (rows)): #This iterates over each index value, i.e. each row, and sums the values and returns them in list format.
v[i] = dfn.loc[i].to_numpy().sum() - sensors
for colname,colitems in df.iteritems():
for rownum,rowitem in colitems.iteritems():
#d[rownum] = dfone.loc[rownum].to_numpy()
#d[colname][rownum] = df.loc[colname][rownum]
if v[rownum] >= sensitivity:
sensors_on = True
off_count = 0
baseline_num[rownum] = 0
else:
sensors_on = False
off_count += 1
if off_count == off_require:
for x in range(0, (off_require)):
baseline_num[colname][rownum] += df[colname][rownum - x]
elif off_count > off_require:
baseline_num[colname][rownum] += baseline_num[colname][rownum - 1] + df[colname][rownum] - (df[colname][rownum - off_require]) #this loop is just an optimization, one calculation per loop once the first calculation is established
baseline[colname][rownum] = ((baseline_num[colname][rownum])//(off_require)) #mean of the last "off_require" points
dfx = DataFrame(v, columns =['Sensor Correlation']) #converts the summed correlation tables back from list format to a DataFrame, with the sole column name 'Sensor Correlation'
dft = pd.DataFrame(baseline, columns =['baseline'])
dft = dft.astype(float)
dfx.plot(figsize=(50,25), linewidth=5, fontsize=40) # plots dfx dataframe which contains correlated and summed data
dft.plot(figsize=(50,25), linewidth=5, fontsize=40)
Basically, instead of 1 graph as this produces, I would like to iterate over each column only for this loop:
for colname,colitems in df.iteritems():
for rownum,rowitem in colitems.iteritems():
#d[rownum] = dfone.loc[rownum].to_numpy()
#d[colname][rownum] = df.loc[colname][rownum]
if v[rownum] >= sensitivity:
sensors_on = True
off_count = 0
baseline_num[rownum] = 0
else:
sensors_on = False
off_count += 1
if off_count == off_require:
for x in range(0, (off_require)):
baseline_num[colname][rownum] += df[colname][rownum - x]
elif off_count > off_require:
baseline_num[colname][rownum] += baseline_num[colname][rownum - 1] + df[colname][rownum] - (df[colname][rownum - off_require]) #this loop is just an optimization, one calculation per loop once the first calculation is established
I've tried some other solutions from other questions but none of them seem to solve this case.
As of now, I've tried multiple conversions to things like lists and tuples, and then calling them something like this:
baseline_num[i,column] += d[i - x,column]
as well as
baseline_num[i][column += d[i - x][column]
while iterating over the loop using
for column in columns
However no matter how I seem to arrange the solution, there is always some keyerror of expecting integer or slice indices, among other errors.
See pictures for expected/possible outputs of one column on actual data.with varying input parameters (sensitivity value, and off_require is varied in different cases.)
One such solution which didn't work was the looping method from this link:
https://www.geeksforgeeks.org/iterating-over-rows-and-columns-in-pandas-dataframe/
I've also tried creating a loop using iteritems as the outer loop. This did not function as well.
Below are links to possible graph outputs for various sensitivity values, and windows in my actual dataset, with only one column. (i.e i manually deleted other columns, and plotted just the one using the current program)
sensitivity 1000, window 8
sensitivity 800, window 5
sensitivity 1500, window 5
If there's anything I've left out that would be helpful to solving this, please let me know so I can rectify it immediately.
See this picture for my original df.head:
df.head
Did you try,
for colname,colitems in df.iteritems():
for rownum,rowitem in colitems.iteritems():
print(df[colname][rownum])
The first loop iterates over all the columns, and the 2nd loops iterates over all the rows for that column.
edit:
From our conversation below, I think that your baseline and df dataframes don't have the same column names because of how you created them and how you are accessing the elements.
My suggestion is that you create the baseline dataframe to be a copy of your df dataframe and edit the information within it from there.
Edit:
I have managed to make your code work for 1 loop, but I run into an index error, I am not sure what your optimisation function does but i think that is what is causing it, take a look.
It is this part baseline_num[colname][rownum - 1], in the second loop i guess because you do rownum (0) -1, you get index -1. You need to change it so that in the first loop rownum is 1 or something, I am not sure what you are trying to do there.
import pandas as pd
import numpy as np
import matplotlib.pyplot as plt
d = {'col1': [-2587.944231, -1897.324231,-2510.304231,-2203.814231,-2105.734231,-2446.964231,-2963.904231,-2177.254231, 2796.354231,-2085.304231], 'col2': [-3764.468462,-3723.608462,-3750.168462,-3694.998462,-3991.268462,-3972.878462,3676.608462,-3827.808462,-3629.618462,-1841.758462,], 'col3': [-166.1357692,-35.36576923, 321.4157692,108.9257692,-123.2257692, -10.84576923, -100.7457692, 89.27423077, -211.0857692, 101.5342308]}
df = pd.DataFrame(data=d)
sensors = 3
window_size = 5
dfn = df.rolling(window_size).corr(pairwise = True)
index = df.index #index of values in the data frame.
rows = len(index) #len(index) returns number of rows in the data.
sensors = 3
baseline_num = [0]*(rows) #baseline numerator, by default zero
baseline = [0]*(rows) #initialize baseline value
baseline = pd.DataFrame(df)
baseline_num = pd.DataFrame(df)
#print(baseline_num)
v = [None]*(rows) # Initialize an empty array v[] equal to amount of rows in .csv file
s = [None]*(rows) #Initialize another empty array for the slope values for detecting when there is an exposure
d = [0]*(rows)
sensors_on = True #Is the sensor detecting something (True) or not (False).
off_count = 0
off_require = 8 # how many offs until baseline is updated
sensitivity = 1000
for i in range(0, (rows)): #This iterates over each index value, i.e. each row, and sums the values and returns them in list format.
v[i] = dfn.loc[i].to_numpy().sum() - sensors
for colname,colitems in df.iteritems():
#print(colname)
for rownum,rowitem in colitems.iteritems():
#print(rownum)
#display(baseline[colname][rownum])
#d[rownum] = dfone.loc[rownum].to_numpy()
#d[colname][rownum] = df.loc[colname][rownum]
if v[rownum] >= sensitivity:
sensors_on = True
off_count = 0
baseline_num[rownum] = 0
else:
sensors_on = False
off_count += 1
if off_count == off_require:
for x in range(0, (off_require)):
baseline_num[colname][rownum] += df[colname][rownum - x]
elif off_count > off_require:
baseline_num[colname][rownum] += baseline_num[colname][rownum - 1] + df[colname][rownum] - (df[colname][rownum - off_require]) #this loop is just an optimization, one calculation per loop once the first calculation is established
baseline[colname][rownum] = ((baseline_num[colname][rownum])//(off_require)) #mean of the last "off_require" points
print(baseline[colname][rownum])
dfx = pd.DataFrame(v, columns =['Sensor Correlation']) #converts the summed correlation tables back from list format to a DataFrame, with the sole column name 'Sensor Correlation'
dft = pd.DataFrame(baseline, columns =['baseline'])
dft = dft.astype(float)
dfx.plot(figsize=(50,25), linewidth=5, fontsize=40) # plots dfx dataframe which contains correlated and summed data
dft.plot(figsize=(50,25), linewidth=5, fontsize=40)
My output looks like this,
-324.0
-238.0
-314.0
-276.0
-264.0
-306.0
-371.0
-806.0
638.0
-412.0
---------------------------------------------------------------------------
ValueError Traceback (most recent call last)
/usr/local/lib/python3.7/dist-packages/pandas/core/indexes/range.py in get_loc(self, key, method, tolerance)
354 try:
--> 355 return self._range.index(new_key)
356 except ValueError as err:
ValueError: -1 is not in range
The above exception was the direct cause of the following exception:
KeyError Traceback (most recent call last)
3 frames
/usr/local/lib/python3.7/dist-packages/pandas/core/indexes/range.py in get_loc(self, key, method, tolerance)
355 return self._range.index(new_key)
356 except ValueError as err:
--> 357 raise KeyError(key) from err
358 raise KeyError(key)
359 return super().get_loc(key, method=method, tolerance=tolerance)
KeyError: -1
I don't have enough rep to comment, but below is what I was able to work out. Hope it helps!
I tried to use the to_list() function while working out an answer, and it threw me an error:
AttributeError: 'DataFrame' object has no attribute 'to_list'
So, I decided to circumvent that method and came up with this:
indexes = [x for x in df.index]
row_vals = []
for index in indexes :
for val in df.iloc[i].values:
row_vals.append(val)
The object row_vals will contain all values in row order.
If you only want to get the row values for a particular row or set of rows, you would need to do this:
indx_subset = [`list of row indices`] #(Ex. [1, 2, 5, 6, etc...])
row_vals = []
for indx in indx_subset:
for val in df.loc[indx].values:
row_vals.append(val)
row_vals will then have all the row values from the specified indices.
I have a very big dataframe with this structure:
Timestamp Val1
Here you can see a real sample:
Timestamp Temp
0 1622471518.92911 36.443
1 1622471525.034114 36.445
2 1622471531.148139 37.447
3 1622471537.284337 36.449
4 1622471543.622588 43.345
5 1622471549.734765 36.451
6 1622471556.2518 36.454
7 1622471562.361368 41.461
8 1622471568.472718 42.468
9 1622471574.826475 36.470
What I want to do is compare the Temp column with itself and if is higher than "X", for example 4, and the time between they is lower than "Y", for example 180 min, then I save some data of they.
Now I'm using two for loops one inside the other, but this expends to much time and usually pandas has an option to avoid this.
This is my code:
cap_time, maxim = 180, 4
cap_time = cap_time * 60
temps= df['Temperature'].values
times = df['Timestamp'].values
results = []
for i in range(len(temps)):
for j in range(i+1, len(temps)):
print(i,j,len(temps))
if float(temps[j]) > float(temps[i])*maxim:
timeIn = dt.datetime.fromtimestamp(float(times[i]))
timeOut = dt.datetime.fromtimestamp(float(times[j]))
diff = timeOut - timeIn
tdiff = diff.total_seconds()
if dd > cap_time:
break
else:
res = [temps[i], temps[j], times[i], times[j], tdiff/60, cap_time/60, maxim]
results.append(res)
break
# Then I save it in a dataframe and another actions
Can Pandas help me to achieve my goal and reduce the execution time? I found dataFrame.diff() but I'm not sure is what I want (or I don`t know how to use it).
Thank you very much.
Short of avoiding the nested for loops, you can already speed things up by avoiding all unnecessary calculations and conversions within the loops. In particular, you can use NumPy broadcasting to define a Boolean array beforehand, in which you can look up whether the condition is met:
import numpy as np
temps_diff = temps - temps[:, None]
times_diff = times - times[:, None]
condition = np.logical_and(temps_diff > maxim,
times_diff < cap_time)
results = []
for i in range(len(temps)):
for j in range(i+1, len(temps)):
if condition[i, j]:
results.append([temps[i], temps[j],
times[i], times[j],
times_diff[i, j]])
results
[[36.443, 43.345, 1622471518.92911, 1622471543.622588, 24.693477869033813],
...
[36.454, 42.468, 1622471556.2518, 1622471568.472718, 12.22091794013977]]
To avoid the loops altogether, you could define a 3-dimensional full results array and then use the condition array as a Boolean mask to filter out the results you want:
import numpy as np
n = len(temps)
temps_diff = temps - temps[:, None]
times_diff = times - times[:, None]
condition = np.logical_and(temps_diff > maxim,
times_diff < cap_time)
results_full = np.stack([np.repeat(temps[:, None], n, axis=1),
np.tile(temps, (n, 1)),
np.repeat(times[:, None], n, axis=1),
np.tile(times, (n, 1)),
times_diff])
results = results_full[np.stack(results_full.shape[0] * [condition])]
results.reshape((5, -1)).T
array([[ 3.64430000e+01, 4.33450000e+01, 1.62247152e+09,
1.62247154e+09, 2.46934779e+01],
...
[ 3.64540000e+01, 4.24680000e+01, 1.62247156e+09,
1.62247157e+09, 1.22209179e+01],
...
])
As you can see, the resulting numbers are the same as above, although this time the results array will contain more rows, because we didn't use the shortcut of starting the inner loop at i+1.
I'm trying to optimize the following code, potentially by rewriting it in Cython: it simply takes a low dimensional but relatively long numpy arrays, looks into of its columns for 0 values, and marks those as -1 in an array. The code is:
import numpy as np
def get_data():
data = np.array([[1,5,1]] * 5000 + [[1,0,5]] * 5000 + [[0,0,0]] * 5000)
return data
def get_cols(K):
cols = np.array([2] * K)
return cols
def test_nonzero(data):
K = len(data)
result = np.array([1] * K)
# Index into columns of data
cols = get_cols(K)
# Mark zero points with -1
idx = np.nonzero(data[np.arange(K), cols] == 0)[0]
result[idx] = -1
import time
t_start = time.time()
data = get_data()
for n in range(5000):
test_nonzero(data)
t_end = time.time()
print (t_end - t_start)
data is the data. cols is the array of columns of data to look for non-zero values (for simplicity, I made it all the same column). The goal is to compute a numpy array, result, which has a 1 value for each row where the column of interest is non-zero, and -1 for the rows where the corresponding columns of interest have a zero.
Running this function 5000 times on a not-so-large array of 15,000 rows by 3 columns takes about 20 seconds. Is there a way this can be sped up? It appears that most of the work goes into finding the nonzero elements and retrieving them with indices (the call to nonzero and subsequent use of its index.) Can this be optimized or is this the best that can be done?
How could a Cython implementation gain speed on this?
cols = np.array([2] * K)
That's going to be really slow. That's create a very large python list and then converts it into a numpy array. Instead, do something like:
cols = np.ones(K, int)*2
That'll be way faster
result = np.array([1] * K)
Here you should do:
result = np.ones(K, int)
That will produce the numpy array directly.
idx = np.nonzero(data[np.arange(K), cols] == 0)[0]
result[idx] = -1
The cols is an array, but you can just pass a 2. Furthermore, using nonzero adds an extra step.
idx = data[np.arange(K), 2] == 0
result[idx] = -1
Should have the same effect.
data is a matrix containing 2500 time series of a measurment. I need to average each time series over time, discarding data points that were recorded around a spike (in the interval tspike-dt*10... tspike+10*dt). The number of spiketimes is variable for each neuron and stored in a dictionary with 2500 entries. My current code iterates over neurons and spiketimes and sets the masked values to NaN. Then bottleneck.nanmean() is called. However this code is to slow in the current version, and I am wondering wheater there is a faster solution. thanks!
import bottleneck
import numpy as np
from numpy.random import rand, randint
t = 1
dt = 1e-4
N = 2500
dtbin = 10*dt
data = np.float32(ones((N, t/dt)))
times = np.arange(0,t,dt)
spiketimes = dict.fromkeys(np.arange(N))
for key in spiketimes:
spiketimes[key] = rand(randint(100))
means = np.empty(N)
for i in range(N):
spike_times = spiketimes[i]
datarow = data[i]
if len(spike_times) > 0:
for spike_time in spike_times:
start=max(spike_time-dtbin,0)
end=min(spike_time+dtbin,t)
idx = np.all([times>=start,times<=end],0)
datarow[idx] = np.NaN
means[i] = bottleneck.nanmean(datarow)
The vast majority of the processing time in your code comes from this line:
idx = np.all([times>=start,times<=end],0)
This is because for each spike, you are comparing every value in times against start and end. Since you have uniform time steps in this example (and I presume this is true in your data as well), it is much faster to simply compute the start and end indexes:
# This replaces the last loop in your example:
for i in range(N):
spike_times = spiketimes[i]
datarow = data[i]
if len(spike_times) > 0:
for spike_time in spike_times:
start=max(spike_time-dtbin,0)
end=min(spike_time+dtbin,t)
#idx = np.all([times>=start,times<=end],0)
#datarow[idx] = np.NaN
datarow[int(start/dt):int(end/dt)] = np.NaN
## replaced this with equivalent for testing
means[i] = datarow[~np.isnan(datarow)].mean()
This reduces the run time for me from ~100s to ~1.5s.
You can also shave off a bit more time by vectorizing the loop over spike_times. The effect of this will depend on the characteristics of your data (should be most effective for high spike rates):
kernel = np.ones(20, dtype=bool)
for i in range(N):
spike_times = spiketimes[i]
datarow = data[i]
mask = np.zeros(len(datarow), dtype=bool)
indexes = (spike_times / dt).astype(int)
mask[indexes] = True
mask = np.convolve(mask, kernel)[10:-9]
means[i] = datarow[~mask].mean()
Instead of using nanmean you could just index the values you need and use mean.
means[i] = data[ (times<start) | (times>end) ].mean()
If I misunderstood and you do need your indexing, you might try
means[i] = data[numpy.logical_not( np.all([times>=start,times<=end],0) )].mean()
Also in the code you probably want to not use if len(spike_times) > 0 (I assume you remove the spike time at each iteration or else that statement will always be true and you'll have an infinite loop), only use for spike_time in spike_times.