I have data from an experiment that is sampling responses between 59 to 60 hz. There is no way to predict the drop-down in sampling rate throughout the experiment which runs for 18 minutes.
Each of the sampled responses are numbered from 1 to N (for total number of rows) showing relative passage of time, stored in variable 'frame'. I also have a unix time stamp marking absolute time stored in 'unixtime'. But unixtime is reported in whole integers & not in fractional units. For example:
1376925380 may be repeated 59 times;
1376925381 may be repeated 60 times in the data file.
I would like to create a new variable that tracks each consecutive frame (or sampled response) from 1 to 60 or from 1 to 59, as the case may be, for each given unixtime stamp in SPSS. See the desired re-arrangement below. Any help w/ appropriate SPSS-syntax is appreciated!
unixtime newframe
1376925380 1
1376925380 2
1376925380 3
1376925380 4
1376925380 5
1376925380 6
....
1376925380 58
1376925380 59
1376925381 1
1376925381 2
1376925381 3
1376925381 4
.... ....
1376925381 60
1376925382 1
1376925382 2
....
If I understand correctly, you can use LAG to figure out your counter between the time stamps. Example below.
*fake data.
set seed 10.
input program.
loop #i = 1 to 100.
loop #j = 1 to TRUNC(RV.UNIFORM(59,61)).
compute unixtime = 1376925379 + #i.
end case.
end loop.
end loop.
end file.
end input program.
*Using lag to calculate newframe variable.
DO IF ($casenum = 1) OR (unixtime <> lag(unixtime)).
compute newframe = 1.
ELSE.
compute newframe = lag(newframe) + 1.
END IF.
exe.
See related discussion for using lag at, Using sequential case processing for data management in SPSS.
Related
As im so new to this field and im trying to explore the data for a time series, and find the missing values and count them and study a distribution of their length and fill in these gaps, the thing is i have, let's say 10 file.txt and for each file i have 2 columns as follows:
C1 C2
944 0
920 1
920 2
928 3
912 7
920 8
920 9
880 10
888 11
920 12
944 13
and so on... lets say till 100 and not necessarily the 10 files have the same number of observations.
so here for example the missing values and not necessarily appears in all files that i have, missing value are: 4,5 and 6 in C2 and the corresponding 1st column C1(measured in milliseconds, so the value of 928ms is not a time neighbor of 912ms). So i want to find those gaps(the total missing values in all 10 files) and show a histogram of their lengths.
i wrote a piece of code in R, but the problem is that i don't get the exact total number that i should have for the missing values.
path = "files path"
out.file<-data.frame(TS = 0, Index = 0, File = '')
file.names <- dir(path, pattern =".txt")
for(i in 1:length(file.names)){
file <- cbind(read.table(file.names[i],
header=F,
sep ="\t",
stringsAsFactors=FALSE),
file.names[i])
colnames(file) <- c('TS', 'Index', 'File')
out.file <- rbind(out.file, file)
}
d = dim(out.file)[1]
misDa = 0
for(i in 2:(d-1)){
if(abs(out.file$Index[i]-out.file$Index[i+1]) > 1)
misDa = misDa+1
}
Hard to give specific hints without having a more extensive example of your data that contains some of the actual NAs.
If you are using R (like it seems) the naniar and the imputeTS packages offer nice functions for missing data visualizations.
Some examples from the naniar package, which is especially good for multivariate data (more plot examples):
Some examples from the imputeTS package, which is especially good for time series data (additional plot examples):
Just looking for some brief advice to put me back on the right track. I have been working on a solution to a problem where I have a very sparse input matrix (~25% of information filled, rest is 0's) stored in a sparse.coo_matrix:
sparse_matrix = sparse.coo_matrix((value, (rater, blurb))).toarray()
After some work on building this array from my data set and messing around with some other options, I currently have my NMF model fitter function defined as follows:
def nmf_model(matrix):
model = NMF(init='nndsvd', random_state=0)
W = model.fit_transform(matrix);
H = model.components_;
result = np.dot(W,H)
return result
Now, the issue is my output doesn't seem to be accounting for the 0 values correctly. Any value that was a 0 gets bumped to some value less than 1 and my known values fluctuate from the actual quite a bit (All data are ratings between 1 and 10). Can anyone spot what I am doing wrong? From the documentation for scikit, I assumed using the nndsvd initialization would help account for the empty values correct. Sample output:
#Row / Column / New Value
35 18 6.50746917334 #Actual Value is 6
35 19 0.580996641675 #Here down are all "estimates" of my function
35 20 1.26498699492
35 21 0.00194119935464
35 22 0.559623469753
35 23 0.109736902936
35 24 0.181657421405
35 25 0.0137801897011
35 26 0.251979684515
35 27 0.613055371646
35 28 6.17494590041 #Actual values is 5.5
Appreciate any advice any more experienced ML coders can offer!
So it seems according to this answer, that the opencv VideoWriter is not really smart (or well, maybe not suited for the purpose I would like to use it) about handling frames. According to the answer of this question, you have to time your frames manually, thus the creation of a two hour long video will take two hours.
If you want to check, the following script creates a 100 fps VideoWriter and writes 1500 frames to it, which should be exactly 15 seconds long, but ends up being 26 seconds or so.
EDIT: The code was edited to create six videos, with 3 fps-s intended to be 15 and 30 seconds long. The table at the end of the question was made using this.
import numpy as np
import cv2
for fps in [20,50,100]:
vWriter = cv2.VideoWriter("test" +str(fps)+".avi", cv2.VideoWriter_fourcc('P','I','M','1'),fps,(500,500),True)
y = 0
for x in range(15*fps):
img = np.zeros((500,500,3)).astype(np.uint8)
cv2.circle(img,(250,int(y)),5,(255,255,255),-1,cv2.LINE_AA)
y += 500/15/fps
vWriter.write(img)
for fps in [20,50,100]:
vWriter = cv2.VideoWriter("test2_" +str(fps)+".avi", cv2.VideoWriter_fourcc('P','I','M','1'),fps,(500,500),True)
y = 0
ts = time.time()
for x in range(30*fps):
img = np.zeros((500,500,3)).astype(np.uint8)
cv2.circle(img,(250,int(y)),5,(255,255,255),-1,cv2.LINE_AA)
y += 500/30/fps
vWriter.write(img)
Is there any workaround for this? This manual timing of frames seems really cumbersome. Or if there are no workarounds, any other cross-platform video creation method that you can recommend, that does not suffer from this problem?
I made a little test with different lengths and framerates, I checked 20, 50 and 100 fps with 15 and 30 second long videos (intended length, so I generated 15 or 30 times the fps frames).
FPS intended_length actual_length
20 15 12
50 15 15
100 15 25
20 30 25
50 30 30
100 30 50
Looks like the 50 fps is the one where it gets it correctly, but why?
I want to subtract a number form a duration but not sure how can I do it.
A1 : 137:47:00 (formatted as duration)
A2 : 126 (formatted as number)
When I subtract it is showing unexpected value
=(A1-A2) = -120.26
I was expecting something similar to 11.
Subtracting a number (without dimension) from a duration does not really make a lot of sense but if 137:47:00 represented 137 hours and 47 minutes then subtracting 126 hours from that would (and give a result between 11 and 12 hours). To be able to compare like with like, the duration can be represented as a number by accessing the fact that Google spreadsheets treats 24 hours as number 1. So multiply 137:47:00 (if representing hour, minutes, seconds) by 24 to get a number from which another number can be subtracted to give a meaningful result (ie 11.7833333 - representing 11 hours 47 minutes if to subtract 126 hours from 137 hours and 47 minutes). Therefore:
=24*A1-A2
might suit.
Calculating time worked per day on Web Applications addresses a vaguely similar issue.
INSERT OVERWRITE TABLE result
SELECT /*+ STREAMTABLE(product) */
i.IMAGE_ID,
p.PRODUCT_NO,
p.STORE_NO,
p.PRODUCT_CAT_NO,
p.CAPTION,
p.PRODUCT_DESC,
p.IMAGE1_ID,
p.IMAGE2_ID,
s.STORE_ID,
s.STORE_NAME,
p.CREATE_DATE,
CASE WHEN custImg.IMAGE_ID is NULL THEN 0 ELSE 1 END,
CASE WHEN custImg1.IMAGE_ID is NULL THEN 0 ELSE 1 END,
CASE WHEN custImg2.IMAGE_ID is NULL THEN 0 ELSE 1 END
FROM image i
JOIN PRODUCT p ON i.IMAGE_ID = p.IMAGE1_ID
JOIN PRODUCT_CAT pcat ON p.PRODUCT_CAT_NO = pcat.PRODUCT_CAT_NO
JOIN STORE s ON p.STORE_NO = s.STORE_NO
JOIN STOCK_INFO si ON si.STOCK_INFO_ID = pcat.STOCK_INFO_ID
LEFT OUTER JOIN CUSTOMIZABLE_IMAGE custImg ON i.IMAGE_ID = custImg.IMAGE_ID
LEFT OUTER JOIN CUSTOMIZABLE_IMAGE custImg1 ON p.IMAGE1_ID = custImg1.IMAGE_ID
LEFT OUTER JOIN CUSTOMIZABLE_IMAGE custImg2 ON p.IMAGE2_ID = custImg2.IMAGE_ID;
I have a join query where i am joining huge tables and i am trying to optimize this hive query. Here are some facts about the tables
image table has 60m rows,
product table has 1b rows,
product_cat has 1000 rows,
store has 1m rows,
stock_info has 100 rows,
customizable_image has 200k rows.
a product can have one or two images (image1 and image2) and product level information are stored only in product table. i tried moving the join with product to the bottom but i couldnt as all other following joins require data from the product table.
Here is what i tried so far,
1. I gave the hint to hive to stream product table as its the biggest one
2. I bucketed the table (during create table) into 256 buckets (on image_id) and then did the join - didnt give me any significant performance gain
3. changed the input format to sequence file from textfile(gzip files) , so that it can be splittable and hence more mappers can be run if hive want to run more mappers
Here are some key logs from hive console. I ran this hive query in aws. Can anyone help me understand the primary bottleneck here ? This job is only processing a subset of the actual data.
Stage-14 is selected by condition resolver.
Launching Job 1 out of 11
Number of reduce tasks not specified. Estimated from input data size: 22
In order to change the average load for a reducer (in bytes):
set hive.exec.reducers.bytes.per.reducer=<number>
In order to limit the maximum number of reducers:
set hive.exec.reducers.max=<number>
In order to set a constant number of reducers:
set mapred.reduce.tasks=<number>
Kill Command = /home/hadoop/bin/hadoop job -kill job_201403242034_0001
Hadoop job information for Stage-14: number of mappers: 341; number of reducers: 22
2014-03-24 20:55:05,709 Stage-14 map = 0%, reduce = 0%
.
2014-03-24 23:26:32,064 Stage-14 map = 100%, reduce = 100%, Cumulative CPU 34198.12 sec
MapReduce Total cumulative CPU time: 0 days 9 hours 29 minutes 58 seconds 120 msec
.
2014-03-25 00:33:39,702 Stage-30 map = 100%, reduce = 100%, Cumulative CPU 20879.69 sec
MapReduce Total cumulative CPU time: 0 days 5 hours 47 minutes 59 seconds 690 msec
.
2014-03-26 04:15:25,809 Stage-14 map = 100%, reduce = 100%, Cumulative CPU 3903.4 sec
MapReduce Total cumulative CPU time: 0 days 1 hours 5 minutes 3 seconds 400 msec
.
2014-03-26 04:25:05,892 Stage-30 map = 100%, reduce = 100%, Cumulative CPU 2707.34 sec
MapReduce Total cumulative CPU time: 45 minutes 7 seconds 340 msec
.
2014-03-26 04:45:56,465 Stage-2 map = 100%, reduce = 100%, Cumulative CPU 3901.99 sec
MapReduce Total cumulative CPU time: 0 days 1 hours 5 minutes 1 seconds 990 msec
.
2014-03-26 04:54:56,061 Stage-26 map = 100%, reduce = 100%, Cumulative CPU 2388.71 sec
MapReduce Total cumulative CPU time: 39 minutes 48 seconds 710 msec
.
2014-03-26 05:12:35,541 Stage-4 map = 100%, reduce = 100%, Cumulative CPU 3792.5 sec
MapReduce Total cumulative CPU time: 0 days 1 hours 3 minutes 12 seconds 500 msec
.
2014-03-26 05:34:21,967 Stage-5 map = 100%, reduce = 100%, Cumulative CPU 4432.22 sec
MapReduce Total cumulative CPU time: 0 days 1 hours 13 minutes 52 seconds 220 msec
.
2014-03-26 05:54:43,928 Stage-21 map = 100%, reduce = 100%, Cumulative CPU 6052.96 sec
MapReduce Total cumulative CPU time: 0 days 1 hours 40 minutes 52 seconds 960 msec
MapReduce Jobs Launched:
Job 0: Map: 59 Reduce: 18 Cumulative CPU: 3903.4 sec HDFS Read: 37387 HDFS Write: 12658668325 SUCCESS
Job 1: Map: 48 Cumulative CPU: 2707.34 sec HDFS Read: 12658908810 HDFS Write: 9321506973 SUCCESS
Job 2: Map: 29 Reduce: 10 Cumulative CPU: 3901.99 sec HDFS Read: 9321641955 HDFS Write: 11079251576 SUCCESS
Job 3: Map: 42 Cumulative CPU: 2388.71 sec HDFS Read: 11079470178 HDFS Write: 10932264824 SUCCESS
Job 4: Map: 42 Reduce: 12 Cumulative CPU: 3792.5 sec HDFS Read: 10932405443 HDFS Write: 11812454443 SUCCESS
Job 5: Map: 45 Reduce: 13 Cumulative CPU: 4432.22 sec HDFS Read: 11812679475 HDFS Write: 11815458945 SUCCESS
Job 6: Map: 42 Cumulative CPU: 6052.96 sec HDFS Read: 11815691155 HDFS Write: 0 SUCCESS
Total MapReduce CPU Time Spent: 0 days 7 hours 32 minutes 59 seconds 120 msec
OK
The query is still taking longer than 5 hours in Hive where as in RDBMS it takes only 5 hrs. I need some help in optimizing this query, so that it executes much faster. Interestingly, when i ran the task with 4 large core instances, the time taken improved only by 10 mins compared to the run with 3 large instance core instances. but when i ran the task with 3 med cores, it took 1hr 10 mins more.
This brings me to the question, "is Hive even the right choice for such complex joins" ?
I suspect the bottleneck is just in sorting your product table, since it seems much larger than the others. I think joins with Hive for tables over a certain size become untenable, simply because they require a sort.
There are parameters to optimize sorting, like io.sort.mb, which you can try setting, so that more sorting occurs in memory, rather than spilling to disk, re-reading and re-sorting. Look at the number of spilled records, and see if this much larger than your inputs. There are a variety of ways to optimize sorting. It might also help to break your query up into multiple subqueries so it doesn't have to sort as much at one time.
For the stock_info , and product_cat tables, you could probably keep them in memory since they are so small ( Check out the 'distributed_map' UDF in Brickhouse ( https://github.com/klout/brickhouse/blob/master/src/main/java/brickhouse/udf/dcache/DistributedMapUDF.java ) For custom image, you might be able to use a bloom filter, if having a few false positives is not a real big problem.
To completely remove the join, perhaps you could store the image info in a keystone DB like HBase to do lookups instead. Brickhouse also had UDFs for HBase , like hbase_get and base_cached_get .