broadinstitute/skopy

skopy

Skopy is an application for image analysis. It’s a lightweight version of CellProfiler.

$ skopy measure skopy/data/metadata.csv --output features.csv

Installation

$ pip install skopy

skopy's Issues

Skopy crashes with IndexError when no ORB features could be detected

wm80f-1a4:label tbecker$ time skopy measure 2014_07_08.csv
  [------------------------------------]    1%
Traceback (most recent call last):
  File "/usr/local/bin/skopy", line 11, in <module>
    load_entry_point('skopy', 'console_scripts', 'skopy')()
  File "/usr/local/lib/python3.6/site-packages/click/core.py", line 722, in __call__
    return self.main(*args, **kwargs)
  File "/usr/local/lib/python3.6/site-packages/click/core.py", line 697, in main
    rv = self.invoke(ctx)
  File "/usr/local/lib/python3.6/site-packages/click/core.py", line 1066, in invoke
    return _process_result(sub_ctx.command.invoke(sub_ctx))
  File "/usr/local/lib/python3.6/site-packages/click/core.py", line 895, in invoke
    return ctx.invoke(self.callback, **ctx.params)
  File "/usr/local/lib/python3.6/site-packages/click/core.py", line 535, in invoke
    return callback(*args, **kwargs)
  File "/Users/tbecker/repos/skopy/skopy/commands/command_measure.py", line 51, in command
    image = skopy.feature.extract(pathname, mask)
  File "/Users/tbecker/repos/skopy/skopy/feature/__init__.py", line 40, in extract
    image.descriptions = describe(x_data)
  File "/Users/tbecker/repos/skopy/skopy/feature/__init__.py", line 27, in describe
    description = Description.measure(index, descriptor)
  File "/Users/tbecker/repos/skopy/skopy/feature/_description.py", line 28, in measure
    "keypoint_x": descriptor.keypoints[index][0],
IndexError: index 2 is out of bounds for axis 0 with size 2

psycopg2 missing in requirements

I did

skopy measure skopy/data/metadata.csv

and got

ModuleNotFoundError: No module named 'psycopg2'

Area value in boxes table has constant value area = 267289

When skopy is used to process / analyze image, the area values are not calculated correctly. The area feature in the "boxes" table has a constant value of 267289.

R code used to read the skopy db

## specify sqlite file 
backend_path <- '/Users/tbecker/Documents/2017_05_22_neutros_sp/workspace/analysis/2014_07_08/measurements.sqlite'

## create db connection 
db <- src_sqlite(path = backend_path)

## table names used by skopy
tbl_name <- list( "boxes", "correlations", "descriptions", "images", "instances", "intensities", "moments", "shapes")

## function to read all tables using lapply
db2table <- function(tbl_name,db){
  tbl(db,tbl_name) %>% collect( n = Inf)
}

## collect data
skopy_db <- lapply(tbl_name, FUN = db2table, db = db) 

min / max values for area

> skopy_db[[1]] %>% summarise(min_area = min(area), max_area = max(area))
# A tibble: 1 x 2
  min_area max_area
     <int>    <int>
1   267289   267289
> 

skopy fails to run with an IndexError: index 2 is out of bounds for axis 0 with size 2

The command skopy measure test.csv fails with

File "/Users/tbecker/repos/skopy_test/skopy/skopy/feature/_description.py", line 28, in measure "keypoint_x": descriptor.keypoints[index][0], IndexError: index 2 is out of bounds for axis 0 with size 2 

ImportError: No module named psycopg2.extensions

The call skopy measure skopy/data/metadata.csv results in an InputError

wm80f-1a4:skopy tbecker$ skopy measure skopy/data/metadata.csv
Traceback (most recent call last):
  File "/usr/local/bin/skopy", line 11, in <module>
    load_entry_point('skopy', 'console_scripts', 'skopy')()
  File "/usr/local/lib/python2.7/site-packages/pkg_resources/__init__.py", line 561, in load_entry_point
    return get_distribution(dist).load_entry_point(group, name)
  File "/usr/local/lib/python2.7/site-packages/pkg_resources/__init__.py", line 2631, in load_entry_point
    return ep.load()
  File "/usr/local/lib/python2.7/site-packages/pkg_resources/__init__.py", line 2291, in load
    return self.resolve()
  File "/usr/local/lib/python2.7/site-packages/pkg_resources/__init__.py", line 2297, in resolve
    module = __import__(self.module_name, fromlist=['__name__'], level=0)
  File "/Users/tbecker/repos/skopy/skopy/__init__.py", line 2, in <module>
    import psycopg2.extensions
ImportError: No module named psycopg2.extensions

After installing psycopg2 using pip (pip install psycopg2) it works

Missing dependencies: pandas, sqlalchemy-utils

Unable to run command skopy --help due to missing dependencies in setup.py