jenti 0.0.1

To create/merge 2D or 3D patches

Patch and Merge

1. Can create patches from both 2D or 3D images
2. Can merge 2D or 3D patches

As for 3D, the primary focus is 3D CT data. The data should be converted to an array before making 3D patches.

So, the 2D image or 3D volume is needed to convert to an array first.

How to install

pip install jenti==0.0.1

pip install jenti

How to use

Sample demonstration on how to use this code is given in test.py and test.ipynb.

How to import

from jenti import patch

Create patches from a 2D image

# Read image
im = Image.open('c.jpg') # color image
im.show()
image = np.array(im) # convert to array

# Create patches
patch_shape = [100, 100]
overlap = [10,10] # overlap between two adjacent patches along both axes
patch = Patch(patch_shape, overlap, patch_name='patch2d', csv_output=True)
patches, info, org_shape = patch.patch2d(image)

# Save patches       
patch.save2d(patches, save_dir='./save2d', ext = '.png')

If the csv_output is set to True, then it will save the locations of each patch in the original image in a csv file.
Patch names will be like: xxxx0000, xxxx0001, xxxx0002, and so on.

Create patches from a 3D volume

# Read volume
data = sio.loadmat('volume.mat')
data = data['data'] # shape: 128 x 128 x 50  x 1

# Create patches
patch_shape = [32, 32, 16, 1] # H x W x D x Ch
overlap = [8, 8, 8, 0]
patch = Patch(patch_shape, overlap, patch_name='patch3d', csv_output=True)
patches, info, org_shape = patch.patch3d(data)

# Save patches
patch.save3d(patches, save_dir='./save3d', ext = '.mat')

Merge 2D patches
Merging can be done in two ways.
Method 1: Read all the patch files first, then merge them together.

# Merge patches
names = os.listdir('./save2d')
patches = []
info = pd.read_csv('patch2d.csv')
info = np.array(info)
org_shape = (3024, 4032, 3)

for name in names:
    p = Image.open(os.path.join('./save2d', name))
    p = np.array(p)
    patches.append(p)
    
merge = Merge(info, org_shape, dtype='uint8')
merged = merge.merge2d(patches)
merged_im = Image.fromarray(merged)
merged_im.show()
merged_im.save('merged2d.png')

Method 2: Provide only the patch directory.

merge = Merge(info, org_shape, dtype='uint8')
merged = merge.merge_from_dir2d('./save2d') 
merged_im = Image.fromarray(merged)
merged_im.show()
merged_im.save('merged2d.png')

Merge 3D patches
Method 1: Read all the patch files first, then merge them together.

# Merge patches
names = os.listdir('./save3d')
patches = []
info = pd.read_csv('patch3d.csv')
info = np.array(info)
org_shape = (128, 128, 50, 1)

for name in names:
    p = sio.loadmat(os.path.join('./save3d', name))
    p = p['p']
    patches.append(p)
    
merge = Merge(info, org_shape, dtype='float32')
merged = merge.merge3d(patches)
sio.savemat('merged3d.mat', {'m': merged}, do_compression=True)

Method 2: Provide only the patch directory.

merge = Merge(info, org_shape, dtype='float32')
merged = merge.merge_from_dir3d('./save3d') 
sio.savemat('merged3d.mat', {'m': merged}, do_compression=True)