gitignore codeluppi

Author: sebastiantiesmeyer

.gitignore

@@ -131,3 +131,5 @@ dmypy.json
 
 # planktonpy files
 *.pl
+
+test/codeluppi-et-al

plankton/utils.py

@@ -0,0 +1,50 @@
+from threading import local
+import numpy as np
+from requests import patch
+from scipy.ndimage import gaussian_filter, maximum_filter
+
+
+
+def get_histograms(sdata, category=None,resolution=5):
+
+    mins = sdata.coordinates.min(0)
+    maxs = sdata.coordinates.max(0)
+
+    n_bins = np.ceil(np.divide(maxs-mins, resolution)).astype(int)
+
+    histograms=[]
+    
+    if category is None:
+        for gene in sdata.genes:
+            histograms.append(np.histogram2d(*sdata[sdata.g==gene].coordinates.T, bins=n_bins, range=([mins[0], maxs[0]], [mins[1], maxs[1]]))[0])
+        
+    else:
+        for c in sdata[category].cat.categories:
+            histograms.append(np.histogram2d(*sdata[sdata[category]==c].coordinates.T, bins=n_bins, range=([mins[0], maxs[0]], [mins[1], maxs[1]]))[0])
+
+    return histograms
+
+
+def ssam(sdata,adata=None,kernel_bandwidth=2.5, patch_length=500):
+
+    patch_delimiters = list(range(0,np.ceil(sdata.x.max()).astype(int),int(patch_length-kernel_bandwidth*3)))+[np.ceil(sdata.x.max()).astype(int)]
+
+    localmax_vectors = []
+    for i,p in enumerate(patch_delimiters[:-1]):
+        hists = get_histograms(sdata.spatial[p:patch_delimiters[i+1]],resolution=1)
+        hists = [gaussian_filter(h,kernel_bandwidth) for h in hists]
+
+        norm=np.sum(hists,axis=0)
+        
+        if adata is None:
+            localmaxs=maximum_filter(norm,size=5)
+            localmaxs = (localmaxs==norm)&(localmaxs!=0)
+            # localmaxs = np.where(localmaxs)
+            localmaxs= [h[localmaxs] for h in hists]
+            localmax_vectors.append(localmaxs)
+        # break
+
+    return localmax_vectors
+    
+
+