Mercurial > repos > imgteam > overlay_images
comparison overlay_images.py @ 4:37662cbf44b8 draft
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/overlay_images/ commit 85185439087caafebf1c75dc78b61a2a1f181225
| author | imgteam |
|---|---|
| date | Fri, 17 Nov 2023 23:34:57 +0000 |
| parents | b74693340624 |
| children | 2495f8b2aefd |
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| 3:22ff7c705a83 | 4:37662cbf44b8 |
|---|---|
| 31 | 31 |
| 32 def get_rgb8_copy(img): | 32 def get_rgb8_copy(img): |
| 33 img = np.squeeze(img) | 33 img = np.squeeze(img) |
| 34 assert img.ndim == 2 or (img.ndim == 3 and img.shape[-1] in (3, 4)) | 34 assert img.ndim == 2 or (img.ndim == 3 and img.shape[-1] in (3, 4)) |
| 35 if str(img.dtype).startswith('float'): | 35 if str(img.dtype).startswith('float'): |
| 36 img = np.round(img * 255).astype('uint8') | 36 img = np.round(img * 255).astype(np.uint8) |
| 37 elif img.dtype == 'uint16': | 37 elif img.dtype == np.uint16: |
| 38 img = img // 256 | 38 img = (img // 256).astype(np.uint8) |
| 39 elif img.dtype != 'uint8': | 39 elif img.dtype != np.uint8: |
| 40 raise ValueError(f'unknown dtype: {img.dtype}') | 40 raise ValueError(f'unknown dtype: {img.dtype}') |
| 41 if img.ndim == 2: | 41 if img.ndim == 2: |
| 42 return np.dstack([img] * 3).copy() | 42 result = np.dstack([img] * 3).copy() |
| 43 else: | 43 else: |
| 44 return img[:, :, :3].copy() | 44 result = img[:, :, :3].copy() |
| 45 assert result.dtype == np.uint8, result.dtype | |
| 46 return result | |
| 45 | 47 |
| 46 | 48 |
| 47 def coloc_vis(in_red_fn, in_green_fn, out_fn): | 49 def coloc_vis(in_red_fn, in_green_fn, out_fn): |
| 48 im1 = read_im_gray(in_red_fn) | 50 im1 = read_im_gray(in_red_fn) |
| 49 im2 = read_im_gray(in_green_fn) | 51 im2 = read_im_gray(in_green_fn) |