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I have a large 3 dimensional (time, longitude, latitude) input array of daily tmax values. I have masked the values which exceed a certain threshold. I need to find those entries where the mask is True for longer than a specific number of (3) consecutive time steps. The result should be a data array with 0s for the nonconsecutive days and numbers corresponding to the length (duration of event) of consecutive elements.
Below is some pseudocode to make myself clearer:
events = find_consecutive(input_array, duration=3)
input_array = [1, 0, 0, 0, 0, 1, 1, 1, 0, 0, 1, 0, 1, 1, 1, 1, 1, 0, 0, 1]
events = [0, 0, 0, 0, 0, 3, 3, 3, 0, 0, 0, 0, 5, 5, 5, 5, 5, 0, 0, 0]
I've had a look at scipy nd image but haven't been able to completely figure out how to use it.
Any help is appreciated :)
Posts: 12
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Joined: Jan 2020
I have a large 3 dimensional (time, longitude, latitude) input array of daily tmax values. I have masked the values which exceed a certain threshold. I need to find those entries where the mask is True for longer than a specific number of (3) consecutive time steps. The result should be a data array with 0s for the nonconsecutive days and numbers corresponding to the length (duration of event) of consecutive elements.
Below is some pseudocode to make myself clearer:
events = find_consecutive(input_array, duration=3)
input_array = [1, 0, 0, 0, 0, 1, 1, 1, 0, 0, 1, 0, 1, 1, 1, 1, 1, 0, 0, 1]
events = [0, 0, 0, 0, 0, 3, 3, 3, 0, 0, 0, 0, 5, 5, 5, 5, 5, 0, 0, 0]
I've had a look at scipy nd image but haven't been able to completely figure out how to use it.
Any help is appreciated :)
Posts: 1,593
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Joined: Jun 2018
Jan132020, 08:07 AM
(This post was last modified: Jan132020, 08:08 AM by perfringo.)
One way of doing it (not that very elegant).
On row #6 unpacking is done and _ value is number of groups which is not needed. Same result can be obtained without unpacking as labels = label(arr)[0]
Rows #6 and 7 can be merged into one but slices = find_objects(label(arr)[0]) it is not so explicit what is going on.
import numpy as np
from scipy.ndimage.measurements import label, find_objects
arr = np.array([1, 0, 0, 0, 0, 1, 1, 1, 0, 0, 1, 0, 1, 1, 1, 1, 1, 0, 0, 1])
labels, _ = label(arr)
slices = find_objects(labels)
for interval in slices:
if 3 <= arr[interval].size:
arr[interval] = arr[interval].size
else:
arr[interval] = 0
arr will be:
Output:
[0 0 0 0 0 3 3 3 0 0 0 0 5 5 5 5 5 0 0 0]
I'm not 'in'sane. Indeed, I am so far 'out' of sane that you appear a tiny blip on the distant coast of sanity. Bucky Katt, Get Fuzzy
Da Bishop: There's a dead bishop on the landing. I don't know who keeps bringing them in here. ....but society is to blame.
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Thanks for your help!
I created a function using the code you shared. However, I get the following error  TypeError: list indices must be integers or slices, not tuple
def consecutive(masked_array):
labels, _ = label(masked_array)
slices = find_objects(labels)
for interval in slices:
xr.where(masked_array[interval].size >= 3, masked_array[interval].size, 0)
return masked_array
Do you know why this may be?
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Jan142020, 09:10 AM
(This post was last modified: Jan142020, 09:10 AM by perfringo.)
I am not consider myself as numpy person. However, (I assume that xr.where is obscure np.where) np.where returns a list of indices:
>>> input_list = [1, 0, 0, 0, 0, 1, 1, 1, 0, 0, 1, 0, 1, 1, 1, 1, 1, 0, 0, 1]
>>> arr = np.array(input_list)
>>> np.where(arr==0)
(array([ 1, 2, 3, 4, 8, 9, 11, 17, 18]),)
>>> arr
array([1, 0, 0, 0, 0, 1, 1, 1, 0, 0, 1, 0, 1, 1, 1, 1, 1, 0, 0, 1]) # array unchanged
>>> np.where(arr[slice(5, 8, None)].size >= 3, 3, 0)
array(3) # we are able to set return value if condition is met
>>> arr
array([1, 0, 0, 0, 0, 1, 1, 1, 0, 0, 1, 0, 1, 1, 1, 1, 1, 0, 0, 1]) # array unchanged
You want to apply new value to slice based on slice length. So you can assign new value to a slice (like in row #7 above):
>>> for interval in slices:
... arr[interval] = np.where(3 <= arr[interval].size, arr[interval].size, 0)
...
>>> arr
array([0, 0, 0, 0, 0, 3, 3, 3, 0, 0, 0, 0, 5, 5, 5, 5, 5, 0, 0, 0])
For better readability size could be assigned to meaningful name:
for interval in slices:
interval_length = arr[interval].size
arr[interval] = np.where(3 <= interval_length, interval_length, 0)
Performance considaration aside I feel that 'pure' Python conditional expression is more understandable:
for interval in slices:
length = arr[interval].size
arr[interval] = length if 3 <= length else 0
With Python 3.8 walrus operator it becomes even more concise:
for interval in slices:
arr[interval] = length if 3 <= (length := arr[interval].size) else 0
I'm not 'in'sane. Indeed, I am so far 'out' of sane that you appear a tiny blip on the distant coast of sanity. Bucky Katt, Get Fuzzy
Da Bishop: There's a dead bishop on the landing. I don't know who keeps bringing them in here. ....but society is to blame.
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Thanks for the explanations!
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(Jan162020, 12:27 AM)chai0404 Wrote: Thanks for the explanations!
You are welcome.
I'm not 'in'sane. Indeed, I am so far 'out' of sane that you appear a tiny blip on the distant coast of sanity. Bucky Katt, Get Fuzzy
Da Bishop: There's a dead bishop on the landing. I don't know who keeps bringing them in here. ....but society is to blame.
Posts: 12
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Joined: Jan 2020
How do I make this work for a 3D array such as the one given below?
input_array([[[1, 1, 0, 0, 0, 1, 1, 1, 1, 0],
[1, 0, 1, 0, 0, 1, 0, 1, 1, 0],
[1, 0, 1, 1, 0, 1, 0, 0, 1, 0]],
[[0, 0, 0, 0, 0, 1, 0, 1, 0, 1],
[0, 1, 1, 1, 0, 0, 0, 0, 1, 0],
[0, 0, 0, 1, 0, 1, 1, 1, 1, 1]]])
output_array([[[1, 1, 0, 0, 0, 4, 4, 4, 4, 0],
[1, 0, 1, 0, 0, 1, 0, 1, 1, 0],
[1, 0, 1, 1, 0, 1, 0, 0, 1, 0]],
[[0, 0, 0, 0, 0, 1, 0, 1, 0, 1],
[0, 3, 3, 3, 0, 0, 0, 0, 1, 0],
[0, 0, 0, 1, 0, 5, 5, 5, 5, 5]]])
I tried this, but it doesn't seem to work 
def consec(temps):
labels, _ = label(temps) # labels the occurrence of 1s and gives it an 'event' number
print (label(temps))
slices = find_objects(labels) # find_objects  what does it do?
print(slices)
new_temps = np.zeros(len(temps))
for i in slices:
if temps[i].size >= 3:
new_temps[i] = new_temps[i].size
else:
new_temps[i] = 0
return new_temps
input_array_3D=input_array
eventss_3D=np.zeros([len(input_array_3D),len(input_array_3D[0]),len(input_array_3D[0][0])]) # check numpy for a more concise
for i in range(len(input_array_3D[0])):
for j in range(len(input_array_3D[0][0])):
#### getting the timeseries of tmax at each pixel with (i,j) Coordination:
input_array_1D=input_array_3D[:,i,j]
##### time series of events for each pixel at (i,j) Coordination
eventss = consec(input_array_1D)
#### gathering all pixels to gethere in 1 array
eventss_3D[:,i,j]=eventss
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Is output example correct? Previously consecutive less than 3 were set to 0, here I observe that in output there are 1 and also 1, 1.
I'm not 'in'sane. Indeed, I am so far 'out' of sane that you appear a tiny blip on the distant coast of sanity. Bucky Katt, Get Fuzzy
Da Bishop: There's a dead bishop on the landing. I don't know who keeps bringing them in here. ....but society is to blame.
Posts: 12
Threads: 4
Joined: Jan 2020
Sorry, you're right. It should be:
input_array([[[1, 1, 0, 0, 0, 1, 1, 1, 1, 0],
[1, 0, 1, 0, 0, 1, 0, 1, 1, 0],
[1, 0, 1, 1, 0, 1, 0, 0, 1, 0]],
[[0, 0, 0, 0, 0, 1, 0, 1, 0, 1],
[0, 1, 1, 1, 0, 0, 0, 0, 1, 0],
[0, 0, 0, 1, 0, 1, 1, 1, 1, 1]]])
output_array([[[0, 0, 0, 0, 0, 4, 4, 4, 4, 0],
[0, 0, 0, 0, 0, 0, 0, 0, 0, 0],
[0, 0, 0, 0, 0, 0, 0, 0, 0, 0]],
[[0, 0, 0, 0, 0, 0, 0, 0, 0, 0],
[0, 3, 3, 3, 0, 0, 0, 0, 0, 0],
[0, 0, 0, 0, 0, 5, 5, 5, 5, 5]]])
