cell-data-loader 0.0.32__py3-none-any.whl

cell_data_loader/util.py

@@ -0,0 +1,892 @@
+#!/usr/bin/python
+
+import os,sys,json,csv,cv2,glob,random,re
+import numpy as np
+from numpy.random import choice,shuffle
+from math import floor,ceil,sqrt
+from PIL import Image,ImageEnhance
+from scipy import ndimage
+from scipy.ndimage.interpolation import map_coordinates
+from scipy.ndimage.filters import gaussian_filter
+from .base_dataset import BaseDataset
+import torch,torchvision
+from contextlib import contextmanager
+import warnings
+#from random import shuffle
+try:
+	from cellpose import models, io
+except:
+	warnings.warn("Working Cellpose not installed -- cell segmentation not"+\
+	" possible")
+
+import skimage
+# DEFINE CELLPOSE MODEL
+
+@contextmanager
+def suppress_stdout():
+    with open(os.devnull, "w") as devnull:
+        old_stdout = sys.stdout
+        sys.stdout = devnull
+        try:  
+            yield
+        finally:
+            sys.stdout = old_stdout
+
+# Function to distort image, stolen shamelessly from
+# https://www.kaggle.com/bguberfain/elastic-transform-for-data-augmentation
+def elastic_transform(im, alpha, sigma, alph_af, rand_s=None):
+	"""Elastic deformation of images as described in [Simard2003]_
+	(with modifications).
+	.. [Simard2003] Simard, Steinkraus and Platt, "Best Practices for
+		 Convolutional Neural Networks applied to Visual Document
+		 Analysis", in Proc. of the International Conference on
+		 Document Analysis and Recognition, 2003.
+	
+	 Based on https://gist.github.com/erniejunior/601cdf56d2b424757de5
+	"""
+	if rand_s is None:
+		rand_s = np.random.RandomState(None)
+	
+	shape = im.shape
+	shape_size = shape[:2]
+	
+	# Random affine
+	cent_squ = np.float32(shape_size) // 2
+	squ_siz = min(shape_size) // 3
+	pts1 = np.float32([cent_squ + squ_siz,
+		[cent_squ[0]+squ_siz, cent_squ[1]-squ_siz], cent_squ - squ_siz])
+	pts2 = pts1 + rand_s.uniform(-alph_af,
+				alph_af, size=pts1.shape).astype(np.float32)
+	M = cv2.getAffineTransform(pts1, pts2)
+	im = cv2.warpAffine(im, M, shape_size[::-1],
+		borderMode=cv2.BORDER_REFLECT_101)
+	
+	dx = gaussian_filter((rand_s.rand(*shape) * 2 - 1), sigma) * alpha
+	dy = gaussian_filter((rand_s.rand(*shape) * 2 - 1), sigma) * alpha
+	dz = np.zeros_like(dx)
+	
+	x, y, z = np.meshgrid(np.arange(shape[1]),\
+				np.arange(shape[0]),\
+				np.arange(shape[2]))
+	indices = np.reshape(y+dy, (-1, 1)),\
+				np.reshape(x+dx, (-1, 1)),\
+				np.reshape(z, (-1, 1))
+	
+	return map_coordinates(im,indices,order=1,mode='reflect').reshape(shape)
+
+def slice_and_augment(im,x,y,l,w,
+		trans = None,
+		out_size = None,
+		rotation=0,
+		x_shift = 0.0,
+		y_shift = 0.0,
+		size_shift = 0.0):
+	"""
+	Slices out and augments a particular cell from a larger image, given
+	the box coordinates (x,y,l <length>, w <width>). The transformation array
+	can be added to augment images as well. The rotation and shifts are applied
+	separately since they may need to consider outside images for the corners.
+	"""
+	if isinstance(im,np.ndarray):
+		dtype = "numpy"
+		imsize = im.shape
+	elif torch.is_tensor(im):
+		dtype = "torch"
+		imsize = im.size()
+	else:
+		raise Exception("Unimplemented type in slice_and_augment")
+	# Random horizontal and vertical shifts
+	x = x + round(max(l,w) * x_shift)
+	y = y + round(max(l,w) * y_shift)
+	
+	# Random size shifts
+	
+	y = int(y - 0.5*(size_shift * w))
+	x = int(x - 0.5*(size_shift * l))
+	l = int(l * (size_shift + 1))
+	w = int(w * (size_shift + 1))
+	
+	# Arbitrary, continuous rotations
+	e   = 2 # sqrt(2)
+	lw  = max(w,l)
+	rr  = range(floor((y + 0.5 * w) - e * lw),ceil((y + 0.5 * w) + e * lw))
+	rr  = [_ % imsize[0] for _ in rr]
+	rr2 = range(floor((x + 0.5 * l) - e * lw),ceil((x + 0.5 * l) + e * lw))
+	rr2 = [_ % imsize[1] for _ in rr2]
+	
+	if dtype == "torch":
+		imslice = torch.index_select(im,0,torch.LongTensor(rr))
+		imslice = torch.index_select(imslice,1,torch.LongTensor(rr2))
+	elif dtype == "numpy":
+		imslice = im.take(rr,axis=0)#,mode='wrap')
+		imslice = imslice.take(rr2,axis=1)#,mode='wrap')
+	else:
+		raise Exception("Unimplemented dtype: %s" % dtype)
+	
+	if dtype == "torch":
+		imshap = imslice.size()
+	elif dtype == "numpy":
+		imshap = imslice.shape
+	else:
+		raise Exception("Unimplemented dtype: %s" % dtype)
+
+	if dtype == "torch":
+		imslice = torchvision.transforms.functional.rotate(imslice,rotation)
+	elif dtype == "numpy":
+		imslice = ndimage.rotate(imslice,rotation)
+	else:
+		raise Exception("Unimplemented dtype: %s" % dtype)
+	
+	# Applies elastic distortion; see above	
+	rr  = range(int(0.5 * imshap[0] - lw/2.0),int(0.5 * imshap[0] + lw/2.0))
+	rr  = [_ % imshap[0] for _ in rr]
+	rr2 = range(int(0.5 * imshap[1] - lw/2.0),int(0.5 * imshap[1] + lw/2.0))
+	rr2 = [_ % imshap[1] for _ in rr2]
+	
+	if dtype == "torch":
+		imslice = torch.index_select(imslice,0,torch.LongTensor(rr))
+		imslice = torch.index_select(imslice,1,torch.LongTensor(rr2))
+	elif dtype == "numpy":
+		imslice = imslice.take(rr,axis=0)#,mode='wrap')
+		imslice = imslice.take(rr2,axis=1)#,mode='wrap')
+	
+	#imslice = Image.fromarray(imslice)
+	if trans is not None: imslice = trans(imslice)
+	
+	#imslice = PIL.ImageEnhance.Color(imslice).enhance(color_shift)
+	
+	#increasing the contrast
+	#new_image = PIL.ImageEnhance.Contrast(image).enhance(1.2)
+	if out_size is not None:
+		if dtype == "torch":
+			imslice = torch.permute(torchvision.transforms.Resize(
+				out_size)(torch.permute(imslice,(2,0,1))),(1,2,0))
+		elif dtype == "numpy":
+			imslice = cv2.resize(imslice,out_size[::-1])
+	return imslice
+
+def get_augmented_image(im,x,y,l,w,output_im_size = (70,70),augment = False,
+	soft_augment = False,c_shift_amt = 0.05,blur_amt = 0.2,
+	spatial_shift_amt = 0.02,elastic_distort = True,size_shift = 0.05,
+	rotate=True,reflect=True,js_params = None,contrast = 0.2,brightness=0.2):
+	
+	if js_params is not None:
+		for k in js_params:
+			p = js_params[k]
+			if k == "blur_amt":
+				blur_amt = int(p)
+			elif k == "spatial_shift_amt":
+				spatial_shift_amt = float(p)
+			elif k == "elastic_distort":
+				elastic_distort = bool(int(p))
+			elif k == "rotate":
+				rotate = bool(int(p))
+			elif k == "reflect":
+				reflect = bool(int(p))
+			elif k == "c_shift_amt":
+				c_shift_amt = bool(int(p))
+			elif k == "size_shift":
+				size_shift = float(p)
+			else:
+				raise Exception("Invalid input parameter %s" %k)
+		
+	c_shift_arr = np.random.rand(3,3)
+	c_shift_arr = c_shift_arr / np.sum(c_shift_arr,axis=1)
+	c_shift_arr = (np.eye(3) * (1-c_shift_amt) + c_shift_arr * c_shift_amt)
+	
+	if augment:
+		imslice = slice_and_augment(im,x,y,l,w,
+		rotation= 0 if not rotate else 360 * np.random.random(),
+		reflection=False if not reflect else choice([True,False]),
+		color_shift = c_shift_arr,
+		blur = 1 + (0.5 - np.random.random()) * 2 * blur_amt,
+		contrast = 1 + (0.5 - np.random.random()) * 2 * contrast,
+		brightness = 1 + (0.5 - np.random.random()) * 2 * brightness,
+		x_shift = (0.5 - np.random.random()) * 2 *spatial_shift_amt,
+		y_shift = (0.5 - np.random.random()) * 2 *spatial_shift_amt,
+		size_shift = size_shift * (np.random.rand() - 0.5),
+		distort = elastic_distort)
+	elif soft_augment:
+		imslice = slice_and_augment(im,x,y,l,w,
+		rotation= 0 if not rotate else 360 * np.random.random(),
+		reflection=False if not reflect else choice([True,False]))
+	else:
+		imslice = slice_and_augment(im,x,y,l,w)
+	if not type(imslice) == Image.Image:
+		imslice = Image.fromarray(imslice)
+	imslice = imslice.resize((output_im_size[0],output_im_size[1]))
+	return imslice
+
+def read_image_file(imfile,out_format = "torch"):
+	basename,ext = os.path.splitext(imfile)
+	if ext.lower() == ".jpg":
+		return
+	elif ext.lower() == ".cz":
+		return
+	elif ext.lower() == ".svz":
+		return
+	return
+
+def read_label_file(label_file):
+	return
+
+def is_image_file(filename):
+	basename,ext = os.path.splitext(filename)
+	return ext.lower() in [".jpg",".png",".jpeg",".czi",".svs",".tiff",".tif"]
+
+def is_label_file(filename):
+	return True
+
+def get_verify(X,Y):
+	h = int(X.shape[1] / 2)
+	w = int(X.shape[2] / 2)
+	q1 = np.expand_dims(np.mean(X[:,:h,:w,:],axis=(1,2,3)),axis=1) / 255.0
+	q2 = np.expand_dims(np.mean(X[:,h:,:w,:],axis=(1,2,3)),axis=1) / 255.0
+	q3 = np.expand_dims(np.mean(X[:,:h,w:,:],axis=(1,2,3)),axis=1) / 255.0
+	q4 = np.expand_dims(np.mean(X[:,h:,w:,:],axis=(1,2,3)),axis=1) / 255.0
+	c1 = np.expand_dims(np.mean(X[:,:,:,0],axis=(1,2)),axis=1) / 255.0
+	c2 = np.expand_dims(np.mean(X[:,:,:,1],axis=(1,2)),axis=1) / 255.0
+	c3 = np.expand_dims(np.mean(X[:,:,:,2],axis=(1,2)),axis=1) / 255.0
+	s  = np.expand_dims(np.std(X,axis=(1,2,3)),axis=1) / 255.0
+	Y_ =  np.concatenate((Y,q1,q2,q3,q4,c1,c2,c3,s),axis=1)
+
+	return Y_
+
+def tile_image(im,autoencoder,a_dims=(600,600)):
+	for i in range(0,im.shape[0],a_dims[0]):
+		for j in range(0,im.shape[1],a_dims[1]):
+			if i+a_dims[0] > im.shape[0]:
+				i = im.shape[0] - a_dims[0] - 1
+			if j+a_dims[1] > im.shape[1]:
+				j = im.shape[1] - a_dims[1] - 1
+			input_im = torch.from_numpy(im[i:i+a_dims[0],
+				j:j+a_dims[1],:]).permute(2,1,0).unsqueeze(0).float()/255.0
+			input_im = autoencoder(input_im)
+			input_im = input_im.squeeze().permute(1,2,0).detach().numpy() * 255.0
+			im[i:i+a_dims[0],j:j+a_dims[1],:] = input_im
+	return im
+
+def get_all_perimeters(mask):
+	perims = {}
+	if len(mask.shape) == 2:
+		for i in np.unique(mask.flatten()):
+			perims[i] = 0
+		for i in range(mask.shape[0]-1):
+			for j in range(mask.shape[1]-1):
+				if mask[i,j] != mask[i+1,j]:
+					perims[mask[i,j]] += 1
+					perims[mask[i+1,j]] += 1
+				if mask[i,j] != mask[i,j+1]:
+					perims[mask[i,j]] += 1
+					perims[mask[i,j+1]] += 1
+	elif len(mask.shape) == 3:
+		for i in range(mask.shape[2]):
+			perims[i] = 0
+	return perims
+
+def get_perimeter(mask):
+	p = 0
+	for i in range(mask.shape[0]-1):
+		for j in range(mask.shape[1]-1):
+			if mask[i,j] != mask[i+1,j]:
+				p += 1
+			if mask[i,j] != mask[i,j+1]:
+				p += 1
+	return p
+
+def get_smoothness(mask,mean_area = None):
+	area = np.sum(mask)
+	#return np.abs(area - mean_area)
+	return float(skimage.measure.perimeter(mask,neighbourhood=4) ** 2)/area
+
+def crop2(dat, clp=True):
+    if clp: np.clip( dat, 0, 1, out=dat )
+    for i in range(dat.ndim):
+        dat = np.swapaxes(dat, 0, i)  # send i-th axis to front
+        while np.all( dat[0]==0 ):
+            dat = dat[1:]
+        while np.all( dat[-1]==0 ):
+            dat = dat[:-1]
+        dat = np.swapaxes(dat, 0, i)  # send i-th axis to its original position
+    return dat
+
+def remove_unsmooth(mask,thresh=25):
+	smoothnesses = np.zeros((len(np.unique(mask))-1,))
+	if len(mask.shape) == 2:
+		for z in np.unique(mask.flatten()):
+			if z > 0:
+				z_mask = crop2(mask == z)
+				smoothnesses[int(z)-1] = get_smoothness(z_mask)
+	elif len(mask.shape) == 3:
+		for z in range(mask.shape[2]):			
+			smoothnesses[z] = get_smoothness(crop2(np.squeeze(mask[:,:,z])))
+	max_smoothness = smoothnesses.max()
+	min_smoothness = smoothnesses.min()
+	for i in range(mask.max()):
+		if smoothnesses[i] > thresh:
+			mask[mask == i+1] = 0
+	mask = renumber_masks(mask)
+	return mask
+
+
+def get_box_intersection_area(bb1,bb2):
+	"""
+	Calculate the Intersection over Union (IoU) of two bounding boxes.
+
+	Parameters
+	----------
+	bb1 : dict
+		Keys: {'x1', 'x2', 'y1', 'y2'}
+		The (x1, y1) position is at the top left corner,
+		the (x2, y2) position is at the bottom right corner
+	bb2 : dict
+		Keys: {'x1', 'x2', 'y1', 'y2'}
+		The (x, y) position is at the top left corner,
+		the (x2, y2) position is at the bottom right corner
+	
+	Returns
+	-------
+	float
+		in [0, 1]
+	-----
+	Adapted from https://stackoverflow.com/questions/25349178/
+	calculating-percentage-of-bounding-box-overlap-for-image-detector-evaluation
+	"""
+	# determine the coordinates of the intersection rectangle
+	bb1_x1 = bb1[1]
+	bb1_x2 = bb1[1] + bb1[3]
+	bb1_y1 = bb1[0]
+	bb1_y2 = bb1[0] + bb1[2]
+	
+	bb2_x1 = bb2[1]
+	bb2_x2 = bb2[1] + bb2[3]
+	bb2_y1 = bb2[0]
+	bb2_y2 = bb2[0] + bb2[2]
+	
+	x_left = max(bb1_x1, bb2_x1)
+	y_top = max(bb1_y1, bb2_y1)
+	x_right = min(bb1_x2, bb2_x2)
+	y_bottom = min(bb1_y2, bb2_y2)
+	
+	if x_right < x_left or y_bottom < y_top:
+		return 0.0
+	
+	# The intersection of two axis-aligned bounding boxes is always an
+	# axis-aligned bounding box
+	intersection_area = (x_right - x_left) * (y_bottom - y_top)
+	
+	# compute the area of both AABBs
+	bb1_area = bb1[3] * bb1[2]
+	bb2_area = bb2[3] * bb2[2]
+
+	# compute the intersection over union by taking the intersection
+	# area and dividing it by the sum of prediction + ground-truth
+	# areas - the interesection area
+	iou = intersection_area / float(bb1_area + bb2_area - intersection_area)
+	assert iou >= 0.0
+	assert iou <= 1.0
+	return iou
+
+def find_box_intersections(annotated_boxes,predicted_boxes,min_dice=0.5):
+	assert(min_dice >= 0.0)
+	assert(min_dice <= 1.0)
+	final_boxes = []
+	for i in range(predicted_boxes.shape[0]):
+		append = True
+		for j in range(annotated_boxes.shape[0]):
+			bb1 = predicted_boxes[i,:]
+			bb2 = annotated_boxes[j,:]
+			dice = get_box_intersection_area(bb1,bb2)
+			if dice > min_dice:
+				append = False
+		if append:
+			final_boxes.append(predicted_boxes[i,:])
+	return np.array(final_boxes)
+
+def merge_predicted_and_annotated(annotated_boxes,predicted_boxes,min_dice=0.5):
+	intersected_boxes = find_box_intersections(annotated_boxes,predicted_boxes,
+		min_dice=min_dice)
+	if intersected_boxes.shape[1] == 4:
+		neg_labels = np.array(["negative" for _ in range(intersected_boxes.shape[0])])
+		neg_labels = np.expand_dims(neg_labels,axis=1)
+		neg_labels = neg_labels.astype(object)
+		intersected_boxes = intersected_boxes.astype(object)
+		intersected_boxes = np.concatenate((intersected_boxes,neg_labels),axis=1)
+	return np.concatenate((annotated_boxes,intersected_boxes),axis=0)
+
+def get_average_mask_size(mask):
+	return np.sum(mask.flatten() > 0) / mask.max()
+
+def renumber_masks(mask):
+	unique_m = np.sort(np.unique(mask))
+	assert(unique_m[0] == 0)
+	if unique_m[-1] == len(unique_m) - 1:
+		return mask
+	for i in range(1,len(unique_m)):
+		mask[mask == unique_m[i]] = i
+	return mask
+
+def remove_edges(mask,min_edge_size=0.5):
+	avg_mask_size = get_average_mask_size(mask)
+	exclude_i = {}
+	for i in range(mask.shape[0]):
+		for j in [0,-1]:
+			val = mask[i,j]
+			if val > 0 and val not in exclude_i:
+				exclude_i[val] = True
+				if np.sum(mask.flatten() == val) < min_edge_size * avg_mask_size:
+					mask[mask == val] = 0
+	for i in range(mask.shape[1]):
+		for j in [0,-1]:
+			val = mask[j,i]
+			if val > 0 and val not in exclude_i:
+				exclude_i[val] = True
+				if np.sum(mask.flatten() == val) < min_edge_size * avg_mask_size:
+					mask[mask == val] = 0
+	mask = renumber_masks(mask)
+	return mask
+
+def remove_smalls(mask,avg_fraction_thresh = 0.5):
+	avg_mask_size = get_average_mask_size(mask)
+	for i in range(1,mask.max() + 1):
+		area = np.sum(mask == i)
+		if area < avg_fraction_thresh * avg_mask_size:
+			mask[mask == i] = 0
+	mask = renumber_masks(mask)
+	return mask
+
+def masks_to_boxes(masks):
+	if len(masks.shape) == 2:
+		num_masks = len(np.unique(masks)) - 1
+	elif len(masks.shape) == 3:
+		num_masks = masks.shape[2]
+	else:
+		raise Exception("Invalid mask length: %d" % len(masks.shape))
+	boxes = np.zeros((num_masks,4),dtype=int)
+	for i in range(num_masks):
+		if len(masks.shape) == 2:
+			y_bar = np.max(masks == i+1,axis=0)
+			x_bar = np.max(masks == i+1,axis=1)
+		elif len(masks.shape) == 3:
+			m = np.squeeze(masks[:,:,i])
+			y_bar = np.max(m,axis=0)
+			x_bar = np.max(m,axis=1)
+		x_min = np.argmax(x_bar)
+		y_min = np.argmax(y_bar)
+		x_max = len(x_bar) - np.argmax(x_bar[::-1]) - 1
+		y_max = len(y_bar) - np.argmax(y_bar[::-1]) - 1
+		boxes[i,0] = y_min
+		boxes[i,1] = x_min
+		boxes[i,2] = y_max - y_min
+		boxes[i,3] = x_max - x_min
+		if i == 1 and False:
+			print(boxes[i,:])
+	return boxes
+
+def get_im(im):
+	if isinstance(im,str) and os.path.isfile(im):
+		return np.array(Image.open(im))
+	elif torch.is_tensor(im):
+		return im.numpy()
+	elif isinstance(im,np.ndarray):
+		return im
+	else:
+		raise Exception("Unsupported type %s" % str(type(im)))
+
+def get_cell_segmentation_mask(imagename,model = None, modelname = "cellpose",gpu=True):
+	if isinstance(imagename,str):
+		save_mask_name = "%s_mask.npy" % os.path.splitext(imagename)[0]
+		if os.path.isfile(save_mask_name):
+			print("Loading mask %s" % save_mask_name)
+			return np.load(save_mask_name)
+	img = get_im(imagename)#img = io.imread(imagename)
+	if model == None:
+		if modelname == "cellpose":
+			try:
+				model = models.Cellpose(gpu=gpu, model_type='cyto')
+			except:
+				raise Exception("""Attempt to instantiate cellpose model 
+					did not work. Please check cellpose dependency""")
+	if modelname == "cellpose":
+		try:
+			masks, flows, styles, diams = model.eval(img, diameter=None,channels=[0,0])
+		except RuntimeError:
+			model = models.Cellpose(gpu=False, model_type='cyto')
+			masks, flows, styles, diams = model.eval(img, diameter=None,channels=[0,0])
+	elif modelname == "deepcell":
+		model = CytoplasmSegmentation()
+		masks = model.predict(img, image_mpp=0.65)
+	if isinstance(imagename,str):
+		print("Saving mask %s" % save_mask_name)
+		np.save(save_mask_name,masks)
+	return masks
+
+
+def get_touch_matrix(unique_vals,mask):
+	unique_vals = list(unique_vals)
+	touch_matrix = np.zeros((len(unique_vals),len(unique_vals))).astype(bool)
+	for i in range(touch_matrix.shape[0]-1):
+		for j in range(touch_matrix.shape[1]-1):
+			if i == j:
+				touch_matrix[i,j] = True
+				touch_matrix[i+1,j+1] = True
+			if mask[i,j] > 0:
+				u1 = unique_vals.index(mask[i,j])
+				for k in [(i,j+1),(i+1,j),(i+1,j+1)]:
+					if mask[k[0],k[1]] > 0:
+						u2 = unique_vals.index(mask[k[0],k[1]])
+						touch_matrix[u1,u2] = True
+						touch_matrix[u2,u1] = True
+	return touch_matrix
+
+def get_all_combos(l,include=None):
+	if include is not None:
+		l2 = list(l.copy())
+		l2.remove(include)
+		l = np.array(l2)
+	all_combinations = []
+	for r in [0,1]:#range(len(l) + 1):
+		combinations_object = itertools.combinations(l, r)
+		combinations_list = [cc for cc in list(combinations_object)]
+		all_combinations += combinations_list
+	if include is not None:
+		all_combinations = [list(l) + [include] for l in all_combinations]
+	return all_combinations
+
+def do_function(mask,mean_area=None):
+	unique_vals = np.unique(mask)
+	unique_vals_list = list(unique_vals)
+	if 0 in unique_vals_list:
+		unique_vals_list.remove(0)
+	else:
+		print("0 not in unique vals")
+	unique_vals = np.array(unique_vals_list)
+	if len(unique_vals) > 10:
+		tm = get_touch_matrix(unique_vals_list,mask)
+	else:
+		tm = None
+	island_mapping = {}
+	for u in unique_vals:
+		if tm is None:
+			all_combo_w_u = get_all_combos(unique_vals,include=u)
+		else:
+			#print(tm)
+			#print(tm[:,unique_vals_list.index(u)].astype(bool))
+			#print(unique_vals)
+			assert(len(unique_vals) == tm.shape[0])
+			combolist = unique_vals[tm[:,unique_vals_list.index(u)]]
+			#print(combolist)
+			if len(combolist) == 1:
+				all_combo_w_u = [[u]]
+			else:
+				all_combo_w_u = get_all_combos(combolist,include=u)
+		print(all_combo_w_u)
+		for c in all_combo_w_u:
+			smoothness = get_smoothness(mask,c,mean_area=mean_area)
+			if u not in island_mapping or island_mapping[u][1] > smoothness:
+				island_mapping[u] = (c,smoothness)
+	ims = [island_mapping[u][0] for u in island_mapping]
+	print("len(ims) %d" % len(ims))
+	ims_nodups = []
+	lolx = {}
+	for im in ims:
+		i_sort = sorted(im)
+		ss = str(i_sort)
+		if ss not in lolx:
+			lolx[ss] = True
+			ims_nodups.append(i_sort)
+	print(ims_nodups)
+	return ims_nodups
+
+def resolve_intersections(masks):
+	mean_area = np.mean([np.sum(masks == i) for i in range(1,masks.max()+1)])
+	labeled_array, num_features = ndimage.label(masks != 0, np.ones((3,3)))
+	all_pairs = []
+	for i in np.unique(labeled_array):
+		mask_copy = masks.copy()
+		mask_copy[labeled_array != i] = 0
+		mask_copy = mask_copy[~np.all(mask_copy == 0,axis=1),:]
+		mask_copy = mask_copy[:,~np.all(mask_copy == 0,axis=0)]
+		print(mask_copy)
+		pairs = do_function(mask_copy,mean_area=mean_area)
+		all_pairs += pairs
+	masks_3D = np.zeros((masks.shape[0],masks.shape[1],len(all_pairs))).astype(bool)
+	print("masks_3D.shape: %s"%str(masks_3D.shape))
+	print("all_pairs len %d" % len(all_pairs))
+	for i in range(len(all_pairs)):
+		pair = all_pairs[i]
+		for p in pair:
+			masks_3D[:,:,i] = np.logical_or(masks_3D[:,:,i],masks == p)
+	print("masks_3D.shape: %s"%str(masks_3D.shape))
+	return masks_3D
+
+def get_cell_boxes_from_image(imagename,model=None,gpu=True,
+	remove_edge_cells=True,return_model=False,verbose=False,
+	do_resolve_intersections=False,do_remove_smalls = True,
+	do_remove_unsmooth=False):
+	#temp = "temp.npy"
+	#if not os.path.isfile(temp) and False:
+	if verbose:
+		masks = get_cell_segmentation_mask(imagename,gpu=gpu,model=model)
+	else:
+		with suppress_stdout():
+			masks = get_cell_segmentation_mask(imagename,gpu=gpu,model=model)
+	if remove_edge_cells:
+		max_m = masks.max()
+		masks = remove_edges(masks,min_edge_size=np.inf)
+		if verbose: print("Removing %d cells from edges" % (max_m - masks.max()))
+	#	np.save(temp,masks)
+	#else:
+	#	masks = np.load(temp)
+	if do_remove_smalls:
+		masks = remove_smalls(masks)
+	# This gave some errors
+	#if do_remove_unsmooth:
+	#	masks = remove_unsmooth(masks)
+	if do_resolve_intersections:
+		print("masks.shape: %s" % str(masks.shape))
+		print("unique_vals len - 1: %d" % (len(np.unique(masks))-1))
+		masks = resolve_intersections(masks)
+	boxes = masks_to_boxes(masks)
+	if return_model:
+		return boxes,masks,model
+	else:
+		return boxes,masks
+
+def get_image_array(imagename,boxes,output_size = (64,64),
+	whole_im_autoencoder=None):
+	image = get_im(imagename)#np.array(Image.open(imagename))
+	if whole_im_autoencoder is not None:
+		image = tile_image(image,whole_im_autoencoder)
+	X = np.zeros((boxes.shape[0],output_size[0],output_size[1],3))
+	for i in range(boxes.shape[0]):
+		x = boxes[i,0]
+		y = boxes[i,1]
+		l = boxes[i,2]
+		w = boxes[i,3]
+		imslice = slice_and_augment(image,x,y,l,w)
+		if not type(imslice) == Image.Image:
+			imslice = Image.fromarray(imslice)
+		imslice = imslice.resize(output_size)
+		imarr = np.expand_dims(np.array(imslice),axis=0)
+		X[i,:,:,:] = imarr
+	return X
+
+def get_predicted_labels(imagename,single_cell_pred_model_filepath='.',
+	gpu=True,remove_edge_cells = True,verbose=True,single_cell_pred_model=None,
+	lb=None,segmodel=None,just_segment = False,autoencoder=None,whole_im_autoencoder=None,
+	use_get_verify = False,num_dropout_tests = 1):
+	if not just_segment and single_cell_pred_model is None and lb is None:
+		single_cell_pred_model,lb = \
+			load_model_w_label_processor(output_folder = \
+			single_cell_pred_model_filepath,get_lb=True)
+	boxes,masks = get_cell_boxes_from_image(imagename,gpu=gpu,model=segmodel)
+	if just_segment:
+		return None,masks
+	X = get_image_array(imagename,boxes,whole_im_autoencoder=whole_im_autoencoder)
+	if autoencoder is not None:
+		X = autoencoder(X)
+	X = X - X.min()
+	X = X / X.max()
+	X = X * 255.0
+	if num_dropout_tests == 1:
+		Y = single_cell_pred_model.predict(X,batch_size=1)
+	else:
+		for layer in single_cell_pred_model.layers:
+			if "dropout" not in layer.name.lower():
+				layer.trainable = False
+		Y_many = np.array(
+				[single_cell_pred_model(X,training=True) for _ in range(num_dropout_tests)]
+			)
+		print(np.std(Y_many,axis=0))
+		Y = np.mean(Y_many,axis=0)
+	Ym = np.argmax(Y[:,:len(lb.classes_)],axis=1)
+	Y_uncertain = np.zeros((Y.shape[0]))
+	for i in range(Y.shape[0]):
+		if np.all(Y[i,:] > 0.0):
+			Y_uncertain[i] = 1
+	#assert(len(np.unique(Ym)) == 2)
+	assert(len(np.unique(masks)) == masks.max() + 1)
+	assert(masks.max() == len(Ym))
+	Ym = np.expand_dims(Ym,axis=1)
+	Yl = lb.inverse_transform(Ym)
+	Yl=np.expand_dims(Yl,axis=1)
+	for i in range(len(Ym)):
+		if Y_uncertain[i] == 1:
+			Yl[i] = "uncertain"
+			masks[masks == i + 1] = -1
+		else:
+			masks[masks == i + 1] = Ym[i] + 1
+	if not use_get_verify:
+		return np.concatenate((boxes,Yl,Y[:,:len(lb.classes_)]),axis=1),masks
+	else:
+		Y = get_verify(X,Y[:,:len(lb.classes_) + 8])
+		return np.concatenate((boxes,Yl,Y),axis=1),masks
+
+def read_in_csv(labels):
+	if isinstance(labels,str) and os.path.isfile(labels):
+		foo = []
+		with open(labels,'r') as fileobj:
+			csvreader = csv.reader(fileobj)
+			for row in csvreader:
+				foo.append(row)
+		labels = foo
+	return labels
+
+def get_classification_percent(labels,class_labels,get_total=False):
+	results = {}
+	total = 0
+	labels = read_in_csv(labels)
+	assert isinstance(labels,list)
+	for c in class_labels:
+		results[c] = 0
+	for row in labels:
+		total += 1
+		l = row[4]
+		results[l] += 1
+	#if results["ring"] > 20: results["ring"] = 0
+	if total == 0:
+		return results
+	if not get_total:
+		for r in results:
+			results[r] = results[r] / total
+	return results
+
+def segment_folder(folderpath,modelpath='.',random_sample=None,
+	output_folderpath = None,model=None,lb=None,segmodel=None,autoencoder=None,
+	whole_im_autoencoder=None,skip_if_present=False,shuffle_order=False):
+	if output_folderpath == None:
+		output_folderpath = folderpath
+	imagenames = glob.glob(os.path.join(folderpath,'*.jpg'))
+	if random_sample is not None:
+		assert(isinstance(random_sample,int) and random_sample > 0)
+		imagenames = list(imagenames)
+		if shuffle_order:shuffle(imagenames)
+		imagenames = imagenames[:random_sample]
+	if not os.path.isdir(output_folderpath):
+		os.makedirs(output_folderpath)
+	for imagename in imagenames:
+		basename = os.path.splitext(os.path.basename(imagename))[0]
+		npy_save = os.path.join(output_folderpath,'%s_predicted.npy'%basename)
+		csv_save = os.path.join(output_folderpath,'%s_predicted.csv'%basename)
+		if os.path.isfile(npy_save) or os.path.isfile(csv_save) \
+			and skip_if_present:
+			continue
+		labels,masks = get_predicted_labels(imagename,
+			gpu=True,
+			single_cell_pred_model_filepath=modelpath,
+			single_cell_pred_model=model,
+			lb=lb,
+			segmodel=None,
+			autoencoder=autoencoder,
+			whole_im_autoencoder=whole_im_autoencoder,
+			use_get_verify = True,num_dropout_tests = 10)
+		#np.save(npy_save,masks)
+		try:
+			np.savetxt(csv_save,labels,delimiter=",",fmt='%s')
+		except:
+			print("Couldn't save the labels")
+
+def get_labelnames_set(label_csv):
+	ll = read_in_csv(label_csv)
+	foo = []
+	for row in ll:
+		foo.append(row[4])
+	return set(foo)
+
+def get_folder_classification(folderpath,get_total=False,get_everything = False):
+	labelnames = glob.glob(os.path.join(folderpath,'*.csv'))
+	class_labels = set([])
+	for labelname in labelnames:
+		class_labels = class_labels.union(get_labelnames_set(labelname))
+	class_labels = sorted(list(class_labels))
+	all_results = {}
+	for labelname in labelnames:
+		result = get_classification_percent(labelname,class_labels,
+			get_total=get_total)
+		if True:#result["ring"] < 16:
+			for r in result:
+				if r not in all_results:
+					all_results[r] = []
+				all_results[r].append(result[r])
+	if get_total and get_everything:
+		return all_results
+	for r in all_results:
+		all_results[r] = float(np.mean(all_results[r]))
+	return all_results
+
+
+def get_file_list_from_str(obj):
+	assert(isinstance(obj, str))
+	if os.path.isfile(obj):
+		if is_image_file(obj):
+			return [obj]
+		else:
+			return []
+	elif os.path.isdir(obj):
+		all_filename_list = []
+		for root, dirs, files in os.walk(obj, topdown=False):
+			for name in files:
+				filename = os.path.join(root, name)
+				if is_image_file(filename):
+					all_filename_list.append(filename)
+		return all_filename_list
+	else:
+		raise Exception("Invalid string input: %s" % obj)
+
+def get_file_list_from_list(obj,allow_list_of_list=True):
+	assert(isinstance(obj,list))
+	if np.all([isinstance(_,list) for _ in obj]):
+		if not allow_list_of_list:
+			raise Exception("Cannot have nested lists")
+		list_of_list = []
+		for l in obj:
+			list_of_list = list_of_list + get_file_list(l,
+				allow_list_of_list = False)
+		return list_of_list
+	elif np.all([isinstance(_,str) for _ in obj]):
+		list_of_str = []
+		for l in obj:
+			list_of_str = list_of_str + get_file_list_from_str(l)
+		return list_of_str
+	else:
+		raise Exception("""Inputs must be strings, lists of lists,
+			or lists of strings""")
+
+def get_file_list(obj,allow_list_of_list=True):
+	if isinstance(obj,str):
+		obj = get_file_list_from_str(obj)
+	elif isinstance(obj,list):
+		obj = get_file_list_from_list(obj)
+	else:
+		raise Exception("Invalid path input")
+	assert(isinstance(obj,list))
+	assert(np.all([isinstance(_,str) for _ in obj]))
+	if np.all([len(_) == 0 for _ in obj]):
+		raise Exception("No valid files found")
+	elif np.any([len(_) == 0 for _ in obj]):
+		raise Exception("One without valid files")
+	return obj
+
+if __name__ == '__main__':
+	imagename = sys.argv[1]
+	output_folder = os.path.join('.','image_segment_examples')
+	just_segment = False
+	if not os.path.isdir(os.path.join('.','models')):
+		just_segment = True
+	if not os.path.isdir(output_folder):
+		os.mkdir(output_folder)
+	foldername = "%s_%s" % (os.path.basename(os.path.dirname(imagename)),
+		os.path.splitext(os.path.basename(imagename))[0])
+	image_output_folder = os.path.join(output_folder,foldername)
+	if not os.path.isdir(image_output_folder):
+		os.mkdir(image_output_folder)
+	labels,masks = get_predicted_labels(imagename,gpu=True,just_segment=just_segment)
+	
+	np.save(os.path.join(image_output_folder,'masks.npy'),masks)
+	if not just_segment:
+		np.save(os.path.join(image_output_folder,'masks_sum.npy'),masks)
+		np.savetxt(os.path.join(image_output_folder,'labels.csv'),labels,
+			delimiter=",",fmt='%s')
+	copyfile(imagename,os.path.join(image_output_folder,os.path.basename(imagename)))
+	print(imagename)