CellProfiler
Export per object classification from a hit table to CSV
After training a classifier and then scoring a dataset, export a CSV file that contains per object classification data. Rows would represent classified objects and, in addition to classification info, there should also be columns for image number and object number.
Checking with @braymp and @dlogan ... does this functionality already exist in CPA? Or did you guys use scripts?
I am actually surprised that we cannot export that as CSV! I always assumed that 'score all' does this already by returning the enrichment scores but I was wrong.
If we don't have this functionality in CPA, I am happy to add it into CPA. The predicted classes are returned in this line of code.
You could use the class_table properties file field, then the TableViewer to open it from the db and subsequently export it.
On Sun, May 29, 2016 at 8:53 AM, David Dao [email protected] wrote:
I am actually surprised that we cannot export that as CSV! I always assumed that 'score all' does this already by returning the enrichment scores but I was wrong.
If we don't have this functionality in CPA, I am happy to add it into CPA. The predicted classes are returned in this line of code https://github.com/CellProfiler/CellProfiler-Analyst/blob/b67352bff3968357c684d19b6c304ef81d3612c4/cpa/multiclasssql.py#L262 .
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We haven't kept up with creating class tables... and I would rather avoid committing to people's databases.
On Sun, May 29, 2016 at 9:32 PM, Mark Bray [email protected] wrote:
You could use the class_table properties file field, then the TableViewer to open it from the db and subsequently export it.
On Sun, May 29, 2016 at 8:53 AM, David Dao [email protected] wrote:
I am actually surprised that we cannot export that as CSV! I always assumed that 'score all' does this already by returning the enrichment scores but I was wrong.
If we don't have this functionality in CPA, I am happy to add it into CPA. The predicted classes are returned in this line of code < https://github.com/CellProfiler/CellProfiler-Analyst/blob/b67352bff3968357c684d19b6c304ef81d3612c4/cpa/multiclasssql.py#L262
.
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Hi Jane,
Silly question: by "new pull request" do you mean that I should sync with the nightly to try out your latest change?
Thanks, Kyle
On Fri, Jun 3, 2016 at 4:41 AM, Jane Hung [email protected] wrote:
There's a new pull request you can try out
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Hi Kyle,
Not quite. It means that you need to start CPA from this branch (scoreAdd_objects). Just download it and run:
python CellProfiler-Analyst.py
(given that your machine has all dependencies installed)
Our automatic build is just for the master branch.
Oh no sorry I should clarify. Pull requests aren't merged in with master, but you can check out the pull request locally to verify the changes are what you're looking for. You can check out using github desktop or command line. On Jun 4, 2016 04:40, "karhohs" [email protected] wrote:
Hi Jane,
Silly question: by "new pull request" do you mean that I should sync with the nightly to try out your latest change?
Thanks, Kyle
On Fri, Jun 3, 2016 at 4:41 AM, Jane Hung [email protected] wrote:
There's a new pull request you can try out
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Could someone confirm the behavior? I guess this would be @karhohs but maybe check w Beth if it's a challenge to check out the right branch.