ExportToDatabase: CellProfiler Analyst Properties File

Usage & Issues
#1

When attempting load into CellProfiler Analyst the properties file generated by the ExportToDatabase module I received this error message:

An error occurred in the program:
AssertionError: PROPERTIES ERROR (image_channel_paths): Field is missing or empty.
Traceback (most recent call last):
File “cpa.py”, line 351, in
File “Properties.pyc”, line 80, in show_load_dialog
File “Properties.pyc”, line 156, in LoadFile
File “Properties.pyc”, line 219, in Validate

I presume this is due to the incorrect elements in the properties file, presumably this is a bug in the module:
“image_path_cols“ should be “image_channel_paths“
“image_file_cols“ should be “image_channel_files“
“image_names“ should be “image_channel_names“

Editing these elements seems to correct the error.

#2

Hi,

Yes, this is due to a prior mismatch between CP and CPA source code. This was corrected in CP r9918; was the version of CP you were running earlier than this?

Regards,
-Mark

Setting image_channel_path correct
#3

Hi,

mbray many thanks for your reply.

This is strange I only downloaded and installed CP and CPA very recently, I’m running CellProfiler_2.0_win32_r9978_beta.exe and CPAnalyst_2.0_r9435_win.exe.

Can you suggest a link to the appropriate versions?

kind regards,
Amos

#4

Hi Amos,

My mistake, I had inferred that you were running CP from our source, and so had the newest version (which is not the case).

As it stands, this is a bug with the workaround that you pointed out. Unfortunately, unless you want to run from the source code (using the latest developer version), it can’t be fixed within the current release. Fortunately, we are planning a new release fairly soon, so this issue will be rectified in that one.

Regards,
-Mark

#5

Hi Mark,
Sorry I’ve only picked up CellProfiler last week – so consider me a total newbie!

I’ll look at the source version & the build instructions.

Rgds,
Amos

#6

For those following this thread: Our latest release, r10415, outputs fields in the properties file with the deprecated names, compatible with the current release of CPA. CPA from source code will automatically recognize these field names and do the right thing.
-Mark