Standard 2p pipeline - initial IO refactor

[landoskape]

In reference to #62, this PR contains:

1. Initial progress on refactoring the IO of suite3d
   • One central s3dio class that handles all data loading operations.
   • Moving around functions from tiff_utils and file_utils to simplify imports and keep related functions in one place.
   • Integration of new s3dio API into the init_pass and iter_step modules.
   • Note: I tested this on the demo files with the AH007_ROI3p33um_NOSCREEN_-400um_00001_00001 header.

Usage (example from init_pass.py module):

jobio = s3dio(job) # created a lightweight IO object that stores the job's parameters and knows how to load data

# since s3dio objects stores a copy of the job, they have access to job.params and know how to load data by default
init_mov = jobio.load_data(init_tifs) 

# note: if one wants to use different params then the one in ``job`` defined at construction,
# the ``s3dio`` method has a mechanism to update parameters on demand - it would look like this:
init_mov = jobio.load_data(init_tifs, **any_updates_to_overwrite_job_params)

# the s3dio object also knows how to load roi_start_pix directly (I think I also made this a bit more efficient)
xs = jobio.load_roi_start_pix()[1]

2. Some "developer tools" I started using for marking code as deprecated or needing attention.
   • Two decorators, @deprecated and @deprecated_inputs that allow us to mark methods that are deprecated or that have deprecated inputs.
   • A todo() method that prints todo messages that need attention, and to highlight places in the code where I think multiple eyes would be useful.
   • Note: all three of these tools will only print anything if os.environ["SUITE3D_DEVELOPER", "").lower() == "true", so that non-developers don't need to see messages related to code management. I added ``os.environ["SUITE3D_DEVELOPER"]="True" to the main Demo notebook with a comment explaining it's purpose.

Usage (another example from init_pass.py module which is deprecated due to the use of the new s3dio module):

@deprecated("Using s3dio.load_data instead")
def load_init_tifs(init_tifs, planes, filter_params, n_ch_tif = 30, convert_plane_ids_to_channel_ids=True, fix_fastZ=False, log_cb=default_log, lbm=True, num_colors=None, functional_color_channel=None):
    """ ... code here ... """

3. Other things:
   • Addition of non-lbm related parameters to default_params.py
   • Smart setting of n_proc_... to make sure it doesn't go above the cores in the machine.
   • Clean up of some unused imports (habit, sorry)
   • Refactor of default_log so it's just defined once

[landoskape]

There's still work to do with handling registration (since we're still hacking our way around LBM related data for the registration part of the pipeline), so this is just a first-pass PR.