Training material for day 2

[saloynton]

The material for the technical training day needs to be finalised. This shall be supported with the findings from the questionnaire sent out to those attending on the second day.

Initially based on what we have at OmeroMatlab, we need to create Java and Python files that contain corresponding code blocks.
E.g. Python:

• Reading_Data.py matlab
  • List Projects. For each, list Datasets and Images
  • Retrieve the projects owned by the user currently logged in.
  • Retrieve the images contained in a dataset.
  • Retrieve an image if the identifier is known.
  • Retrieve Screening data
  • Retrieve Wells within a Plate
  • Retrieve information about an image for example to draw it.
  • Retrieve a pixels set if id is known

• Raw Data Access.py matlab
  • Retrieve a given plane
  • Retrieve a given stack
  • Retrieve a given hypercube

• Write_Data.py matlab
  • How to create a file annotation and link to an image
  • Load all the annotations with a given namespace linked to images
  • Read the attachment

• ROIs.py
  • Retrieve ROIs linked to an Image.
  • Create ROI

• Delete data.py
  • Delete Image

[wmoore]

Python code is under squig/team/Training/ along with script that parses code samples and generates wiki.

E.g. this code

# Retrieve a given stack

# Get all the planes in a Z-stack.

c,t = 0,0       # First channel and timepoint
zctList = [(z, c, t) for z in range(sizeZ)]     # list of [ (0,0,0), (1,0,0), (2,0,0)....etc... ]
print "\nZ stack of planes:"
planes = pixels.getPlanes(zctList)
for i, p in enumerate(planes):
    print "plane zct:", zctList[i], " min:", p.min(), " max:", p.max()

generates this wiki text

• Retrieve a given stack

Get all the planes in a Z-stack.

c,t = 0,0       # First channel and timepoint
zctList = [(z, c, t) for z in range(sizeZ)]     # list of [ (0,0,0), (1,0,0), (2,0,0)....etc... ]
print "\nZ stack of planes:"
planes = pixels.getPlanes(zctList)
for i, p in enumerate(planes):
    print "plane zct:", zctList[i], " min:", p.min(), " max:", p.max() 

[wmoore]

We are working on Python code here:
​https://github.com/will-moore/openmicroscopy/tree/feature/training_examples

JM: you wanna put other samples there too? We can move the location later if we decide to.