From e2404833441fe4e6369751720cea03d090b578f1 Mon Sep 17 00:00:00 2001
From: Ali Khan <alik@robarts.ca>
Date: Tue, 8 Oct 2024 08:40:49 -0400
Subject: [PATCH] cleanout unused lib/dask_image.py

---
 workflow/lib/dask_image.py          | 45 -----------------------------
 workflow/scripts/tif_to_zarr.py     |  1 -
 workflow/scripts/tif_to_zarr_gcs.py |  1 -
 3 files changed, 47 deletions(-)
 delete mode 100644 workflow/lib/dask_image.py

diff --git a/workflow/lib/dask_image.py b/workflow/lib/dask_image.py
deleted file mode 100644
index dbc06c3..0000000
--- a/workflow/lib/dask_image.py
+++ /dev/null
@@ -1,45 +0,0 @@
-from __future__ import annotations
-
-import os
-from glob import glob
-
-try:
-    import tifffile
-except (AttributeError, ImportError):
-    pass
-
-from dask.array.core import Array
-from dask.base import tokenize
-
-
-def add_leading_dimension(x):
-    return x[None, ...]
-
-def imread(fn, page):
-    return tifffile.imread(fn,key=page)
-
-
-def imread_pages(filename, preprocess=None):
-
-    
-    tif = tifffile.TiffFile(filename)
-    pages = [i for i in range(len(tif.pages))]
-    name = "imread-%s" % tokenize(filename, os.path.getmtime(filename))
-
-    sample = tif.pages[0].asarray()
-
-    if preprocess:
-        sample = preprocess(sample)
-
-    keys = [(name, i) + (0,) * len(sample.shape) for i in pages]
-    if preprocess:
-        values = [
-            (add_leading_dimension, (preprocess, (imread, filename,i))) for i in pages
-        ]
-    else:
-        values = [(add_leading_dimension, (imread, filename,i)) for i in pages]
-    dsk = dict(zip(keys, values))
-
-    chunks = ((1,) * len(pages),) + tuple((d,) for d in sample.shape)
-
-    return Array(dsk, name, chunks, sample.dtype)
diff --git a/workflow/scripts/tif_to_zarr.py b/workflow/scripts/tif_to_zarr.py
index 034a9cb..8787c9f 100644
--- a/workflow/scripts/tif_to_zarr.py
+++ b/workflow/scripts/tif_to_zarr.py
@@ -5,7 +5,6 @@
 import dask.array as da
 from dask.delayed import delayed
 from dask.array.image import imread as imread_tifs
-from lib.dask_image import imread_pages
 from itertools import product
 from dask.diagnostics import ProgressBar
 
diff --git a/workflow/scripts/tif_to_zarr_gcs.py b/workflow/scripts/tif_to_zarr_gcs.py
index ac6ac93..4e1d642 100644
--- a/workflow/scripts/tif_to_zarr_gcs.py
+++ b/workflow/scripts/tif_to_zarr_gcs.py
@@ -8,7 +8,6 @@
 import dask.array.image 
 from itertools import product
 from dask.diagnostics import ProgressBar
-from lib.dask_image import imread_pages
 import gcsfs
 import pyvips
 from snakemake.io import expand