WHY IS THIS CHANGE NEEDED?:
- a case in which x and y dimensions are unequal is better at revealing
  dimension storage/conversion issues

HOW DOES THE CHANGE SOLVE THE PROBLEM?:
- tile existing image to size x = 1800, y = 1200

WHAT SIDE EFFECTS DOES THIS CHANGE HAVE?:
- filenames have changed

EVIDENCE THAT COMMIT WORKS:
- doesn't seem to break existing tests, specifically test_image.py and test_tiler.py

WHY IS THIS CHANGE NEEDED?:
- TypeError raised when Tiler.dummy object was instantiated ('method'
  object is not iterable)

HOW DOES THE CHANGE SOLVE THE PROBLEM?:
- dummy_omero_metadata was a tuple of dicts, changed it to a dict.  this
  also makes available the .update() method of a dict.  and is also
  consistent with the datatype it should be in the return statement.

EVIDENCE THAT COMMIT WORKS:
- Tiler.dummy object can be instantiated from a parametes dict without
  errors

REFERENCES:
- issue #62

WHY IS THIS CHANGE NEEDED?:
- using dev_testimage.py in skeletons: when dummy tiler is created and
  tiler.initialise_traps() is invoked, segment_traps() (still) raises 'No valid
  'tiling regions found'

HOW DOES THE CHANGE SOLVE THE PROBLEM?:
- in tiler.initialise_traps(), initial_image was defined based on
  self.ref_channel and self.ref_z; however, if ref_z was not 0, then
  initial_image would be a zero array.
- this was because ImageDummy.pad_array() put the input image at the 0
  position and pads with zeros regardless of the value of ref_z.
- so i wanted the output of ImageDummy.get_data_lazy() to be defined in
  such a way that the (ref_z)th slice in the z-direction is the input
  image.
- therefore, i added a new argument to Image.Dummy.pad_array() so
  that ref_z can be used to achieve the above.

WHAT SIDE EFFECTS DOES THIS CHANGE HAVE?:
- tech debt: no (easy) way to deal with ref_channel because it's a
  string.  workaround is to keep the ref_channel the first channel
  in the dummy tiler, and assume that throughout.

EVIDENCE THAT COMMIT WORKS:
- modified test_image.py works
- skeletons: dummy tiler can be defined and dummy_tiler._run_tp(0) runs
  without errors

WHY IS THIS CHANGE NEEDED?:
- when tiler.initialise_traps() is invoked, "No valid tiling regions
  found" is raised from traps.segment_traps() (aliby.tile.traps).

HOW DOES THE CHANGE SOLVE THE PROBLEM?:
- the image called by segment_traps() was a blank image.
- this was because tiler.initialise_traps() uses the first timepoint to
  define the initial image (line 400 in tiler.py).
- the first timepoint was a blank image because ImageDummy.pad_array()
  added zero arrays BEFORE the input array.
- so fixed it by reversing the behaviour of ImageDummy.pad_array()
- and modified the test_image test to reflect this change.

WHAT SIDE EFFECTS DOES THIS CHANGE HAVE?:
- none known -- only potential effect is the test, which was modified

EVIDENCE THAT COMMIT WORKS:
- test_image passed

WHY IS THIS CHANGE NEEDED?:
- tiler dimensions are ctzyx, but image dimensions are tczyx by default.
  this leads to incorrect storage of shapes

HOW DOES THE CHANGE SOLVE THE PROBLEM?:
- re-arrange the dimensions in the shape property to match image
- justifying this for the purpose of getting ImageDummy to play well
  with Tiler

WHAT SIDE EFFECTS DOES THIS CHANGE HAVE?:
- this exposes technical debt: there are places in which the order of
  dimensions are hard-coded and later assumed like this, and leads to
  indexing dimensions by index rather than by name.  in addition, the
  assumed order of dimensions is inconsistent throughout tiler.  this is
  a recipe for confusion.  worth a refactor soon.

WHY IS THIS CHANGE NEEDED?:
- when new slices are added using ImageDummy.pad_array(), the original
  array is at the end

HOW DOES THE CHANGE SOLVE THE PROBLEM?:
- for consistency, made the 'nil' elements precede the reference channel

WHY IS THIS CHANGE NEEDED?:
- it complained that ImageDummy object has no .shape attribute when
  Tiler methods like ._run_tp() were called

HOW DOES THE CHANGE SOLVE THE PROBLEM?:
- first argument of the object to be returned by .dummy() is mistakenly
  an Image instance (i.e. ImageDummy); it should be a dask array like
  those returned by e.g. .from_image(), .from_h5()
- fixed by using the .data attribute, consistent with the other methods mentioned

WHAT SIDE EFFECTS DOES THIS CHANGE HAVE?:
- order of dimensions is inconsistent: it is tczxy in io.image.py but
  ctzxy in the .shape() method in tiler.py.  this may break things down
  the line

WHY IS THIS CHANGE NEEDED?:
- consistency

HOW DOES THE CHANGE SOLVE THE PROBLEM?:
- fill in unspecified channels with 'nil' -- normally this information
  is fetched from metadata, which we don't have for this dummy

WHY IS THIS CHANGE NEEDED?:
- currently has one time point, one channel, one z-stack and thus
  mimicking usual Image.data structure.  this isn't what we want to test.

HOW DOES THE CHANGE SOLVE THE PROBLEM?:
- use pad_array() to pad with zeros so that the shape is as desired

REFERENCES:
- MR !10

WHY IS THIS CHANGE NEEDED?:
- not obvious that there is an example

HOW DOES THE CHANGE SOLVE THE PROBLEM?:
- highlight example in ```
- remove unnecessary example detail that isn't needed to understand the function

REFERENCES:
- MR !10

HOW DOES THE CHANGE SOLVE THE PROBLEM?:
- remove FIXME

REFERENCES:
- MR !10

WHY IS THIS CHANGE NEEDED?:
- test dummy tiler, see if it crashes

REFERENCES:
- issue #53

REFERENCES:
- issue #53

WHY IS THIS CHANGE NEEDED?:
- need to test whether ImageDummy object makes Tiler happy
- existing implementation lacked a metadata argument, which Tiler expected

HOW DOES THE CHANGE SOLVE THE PROBLEM?:
- create a dummy_omero_metadata dict, based on the arguments of the
  metadata() property of the Image object from aliby.io.omero

WHAT SIDE EFFECTS DOES THIS CHANGE HAVE?:
- metadata dict is hard-coded, ideally take some info from ImageDummy
  object and parameters
- instantiating Tiler raises "Tiler: No z_perchannel data: 'zsections'",
  and several attributes are missing -- this may be expected

EVIDENCE THAT COMMIT WORKS:
- need to write tests, not sure what we should be looking for.  at the
  very least, an instantiation that doesn't break

REFERENCES:
- issue #53

WHY IS THIS CHANGE NEEDED?:
- consistent with standard indexing, and should make tiler happy

HOW DOES THE CHANGE SOLVE THE PROBLEM?:
- get the z-dimension in

REFERENCES:
- issue #53

WHY IS THIS CHANGE NEEDED?:
- https://git.ecdf.ed.ac.uk/swain-lab/aliby/aliby/-/jobs/56786 because
  AttributeError: 'function' object has no attribute 'shape'

REFERENCES:
- issue #53

WHY IS THIS CHANGE NEEDED?:
- https://git.ecdf.ed.ac.uk/swain-lab/aliby/aliby/-/jobs/56781 failed

REFERENCES:
- issue #53

WHY IS THIS CHANGE NEEDED?:
- https://git.ecdf.ed.ac.uk/swain-lab/aliby/aliby/-/jobs/56767 failed
  because ValueError: The truth value of a Array is ambiguous.

HOW DOES THE CHANGE SOLVE THE PROBLEM?:
- use numpy.array_equal() to compare arrays instead

REFERENCES:
- issue #53

WHY IS THIS CHANGE NEEDED?:
- https://git.ecdf.ed.ac.uk/swain-lab/aliby/aliby/-/jobs/56762 failed
  because TypeError: compute() takes 1 positional argument but 2 were given

HOW DOES THE CHANGE SOLVE THE PROBLEM?:
- corrected a stupid typo: compute() is a function that takes no
  arguments that gives out an array, and i want to index that array

REFERENCES:
- issue #53

WHY IS THIS CHANGE NEEDED?:
- https://git.ecdf.ed.ac.uk/swain-lab/aliby/aliby/-/jobs/56757 failed
  because TypeError raised: 'int' object is not iterable

HOW DOES THE CHANGE SOLVE THE PROBLEM?:
- @pytest.mark.parametrize() takes an iterable, e.g. a list -- I forgot
  about it.  fixed it by putting the values in a list.

REFERENCES:
- issue #53

EVIDENCE THAT COMMIT WORKS:
- issue #53

REFERENCES:

REFERENCES:
- issue #53

WHY IS THIS CHANGE NEEDED?:
- to help create a dummy image instance with dimensions tiler likes

HOW DOES THE CHANGE SOLVE THE PROBLEM?:
- decided to separate these two steps: (1) add more dimensions to loaded
  image, (2) pad the dask array.  otherwise, i'd have to tell the
  pad_array function the existing dimensions -- it's easier to just
  assume it has five before running
- pad_array: just concat zero arrays with same dimensions as image_array

REFERENCES:
- issue #53

WHY IS THIS CHANGE NEEDED?:
With numpy version 1.21.6 the pipeline was failing to complete because the statement at line 567 of writer.py:
 if (
                df.columns.dtype == np.int
                or df.columns.dtype == np.dtype("uint")
                or df.columns.name == "timepoint"
            ):
was false - this was due to a mismatch between the numpy and pandas integer data types. This might be fixed if the correct version of numpy is used. On windows this seems to be affected by the installation of omero-py

HOW DOES THE CHANGE SOLVE THE PROBLEM?:
The if statement is removed so the timepoint column is always written

EVIDENCE THAT COMMIT WORKS:
Whole pipeline now works with unit test on Windows 10 (sce-bio-c04115)

WHY IS THIS CHANGE NEEDED?:
- an overview of what image instances do will help us understand and use
  such objects

HOW DOES THE CHANGE SOLVE THE PROBLEM?:
- add long docstring at beginning of module (similar to e.g. tiler)
- modify line in docstring for ImageDir.  it doesn't inherit from
  ImageLocal; it inherits from BaseLocalImage.

WHAT SIDE EFFECTS DOES THIS CHANGE HAVE?:
- need to check whether descriptions are accurate

WHY IS THIS CHANGE NEEDED?:
- organise notes from last commit & give context to writing code

REFERENCES:
- issue #53

WHY IS THIS CHANGE NEEDED?:
- organise notes from last commit & provide context to help with
  developing code

REFERENCES:
- issue #53

- clarification of what needs to be done as comments/docstrings

REFERENCES:
- issue #53

WHY IS THIS CHANGE NEEDED?:
- need a way to produce a dummy form of the next step after creating an
  image instance to test pipeline; this next step is the tiler

HOW DOES THE CHANGE SOLVE THE PROBLEM?:
- make template method

REFERENCES:
- issue #53

WHY IS THIS CHANGE NEEDED?:
- need function that creates the expected output from dummy image file,
  as an interface for other classes' get_data_lazy() methods

HOW DOES THE CHANGE SOLVE THE PROBLEM?:
- create abstract method that loads the dummy image file and returns
  2d dask array
- define function to get examples directory, following logfile_parser.legacy

WHAT SIDE EFFECTS DOES THIS CHANGE HAVE?:
- only able to handle one TIF file (i.e. 1 z-section)

EVIDENCE THAT COMMIT WORKS:
- created a test class that extends BaseLocalImage and has a
  get_data_lazy() function that extends the base class's function; it is
  able to load the dummy image into a dask array

REFERENCES:
- issue #53

WHY IS THIS CHANGE NEEDED?:
- need a TIFF image file to serve as a dummy image input for dummy image
  processing functions

HOW DOES THE CHANGE SOLVE THE PROBLEM?:
- add TIFF file from unit test (staffa:560)

REFERENCES:
- issue #53