NEW: Add DICOM Read Support

[John-P]

Main Changes

1. Add a new DICOMWSIReader for reading DICOM WSIs. Very similar to OpenSlideWSIReader.
   • Add new sample DICOM image to the toolbox samples server by converting CMU-1.svs with wsidicomizder and zipping it.
   • Update function for fetching remote samples to enable downloading of a zip (as the DICOM WSI is a directory) and unzipping it after download.
2. Refactor some code to fix linter issues, reduce complexity, and move private functions
   from WSIReader to WSIMeta where appropriate.
   • Move level_downsample to WSIMeta to calculate the downsample for a level as it only requires access to information in the metadata object (sizes of levels in the pyramid).
   • Move relative_level_scales to WSIMeta as it only depends on level_downsample and data from the metadata object.

Additional Changes

• DICOM terms added to whitelist.
• This PR now also updates some requirements constraints in response to comments.
• Pre-commit config for black updated due to CI issues.

[codecov]

Codecov Report

Merging #270 (4ff3151) into develop (47b9494) will increase coverage by 0.00%.
The diff coverage is 99.24%.

@@           Coverage Diff            @@
##           develop     #270   +/-   ##
========================================
  Coverage    99.81%   99.82%           
========================================
  Files           53       53           
  Lines         4934     5003   +69     
  Branches       816      824    +8     
========================================
+ Hits          4925     4994   +69     
  Misses           2        2           
  Partials         7        7           

Impacted Files	Coverage Δ
tiatoolbox/wsicore/wsireader.py	99.22% <98.75%> (+0.02%)	⬆️
tiatoolbox/data/__init__.py	100.00% <100.00%> (ø)
tiatoolbox/wsicore/wsimeta.py	100.00% <100.00%> (ø)
tiatoolbox/tools/stainextract.py	100.00% <0.00%> (ø)

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[John-P]

@shaneahmed Looks like it's just black causing it to fail now. Fixed the coverage to 100% on patch.

[shaneahmed]

Nice work!
Looks good to me. A few changes and we should be ready to merge.

[shaneahmed]

I am leaving this to your judgement otherwise I am approving this PR.
#270 (comment)

[vqdang]

Minor comments. Why do I see here and there edit within TiffReader? Also, some helper function may perhap should be migrated to base class in the future (us time validation, shape conversion)

[John-P]

@vqdang I have not modified TiffReader. It may have been caused by someone merging changes merged in from develop or from a change in the Black style guide which happened during this PR e.g. 2**n now becomes 2 ** n.

[shaneahmed]

@vqdang I have not modified TiffReader. It may have been caused by someone merging changes merged in from develop or from a change in the Black style guide which happened during this PR e.g. 2**n now becomes 2 ** n.

I merged these as the new version of black fails on 2 ** n you won't be able to pass this PR until you make this change or keep old version of black.

[John-P]

@vqdang I have not modified TiffReader. It may have been caused by someone merging changes merged in from develop or from a change in the Black style guide which happened during this PR e.g. 2**n now becomes 2 ** n.

I merged these as the new version of black fails on 2 ** n you won't be able to pass this PR until you make this change or keep old version of black.

Ah yes I just mixed up the way round the change happened for **