Update v1.47

starparser/__init__.py

@@ -1,4 +1,4 @@
 import os
 
-__version__ = '1.45'
+__version__ = '1.47'
 _ROOT = os.path.abspath(os.path.dirname(__file__))

starparser/columnplay.py

@@ -27,7 +27,7 @@ def delcolumn(particles, columns, metadata):
         The "1" tells .drop that it is the column axis that we want to drop
         inplace means we want the dataframe to be modified instead of creating an assignment
         """
-        nocolparticles.drop(c, 1, inplace=True)
+        nocolparticles.drop(c, axis=1, inplace=True)
 
         #We nead to remove that column header too. The heads are the third
         #metadata (i.e. metadata[3])
@@ -77,7 +77,7 @@ def swapcolumns(original_particles, swapfrom_particles, columns):
         The "1" means the column axis and inplace means the dataframe
         should be modified instead of creating an assignment
         """
-        swappedparticles.drop(c,1,inplace=True)
+        swappedparticles.drop(c,axis=1,inplace=True)
 
         """
         Insert the new column in the right index using .insert()
@@ -140,7 +140,7 @@ def importmicvalues(importedparticles, importfrom_particles, column):
         The "1" tells .drop that it is the column axis that we want to drop
         inplace means we want the dataframe to be modified instead of creating an assignment
         """
-        importedparticles.drop("_rlnMicrographNameSimple", 1, inplace=True)
+        importedparticles.drop("_rlnMicrographNameSimple", axis=1, inplace=True)
 
     return(importedparticles)
 
@@ -293,7 +293,7 @@ def replacecolumn(particles,replacecol,newcol):
     The "1" means the column axis and inplace means the dataframe
     should be modified instead of creating an assignment
     """
-    particles.drop(replacecol, 1, inplace=True)
+    particles.drop(replacecol, axis=1, inplace=True)
 
     #Insert the new column in the right index using .insert()
     #Since newcol comes in as a list, we don't have to modify it

starparser/particleplay.py

@@ -41,8 +41,8 @@ def limitparticles(particles, column, limit, operator):
     elif operator == "le":
         limitedparticles = limitedparticles[limitedparticles[tempcolumnname]<=limit]
 
-    particles.drop(tempcolumnname,1, inplace=True)
-    limitedparticles.drop(tempcolumnname,1, inplace=True)
+    particles.drop(tempcolumnname, axis=1, inplace=True)
+    limitedparticles.drop(tempcolumnname, axis=1, inplace=True)
 
     if len(limitedparticles.index) == 0:
         print("\n>> Error: there are no particles that match the criterion.\n")
@@ -74,10 +74,10 @@ def delparticles(particles, columns, query, queryexact):
 
     if not queryexact:
         q = "|".join(query)
-        purgedparticles.drop(purgedparticles[purgedparticles[columns[0]].str.contains(q)].index , 0,inplace=True)
+        purgedparticles.drop(purgedparticles[purgedparticles[columns[0]].str.contains(q)].index , axis=0,inplace=True)
     else:
         for q in query:
-            purgedparticles.drop(purgedparticles[purgedparticles[columns[0]]==q].index , 0,inplace=True)
+            purgedparticles.drop(purgedparticles[purgedparticles[columns[0]]==q].index , axis=0,inplace=True)
 
     return(purgedparticles)
 
@@ -94,7 +94,7 @@ def delduplicates(particles, column):
 def delmics(particles, micstodelete):
     purgedparticles = particles.copy()
     m = "|".join(micstodelete)
-    purgedparticles.drop(purgedparticles[purgedparticles["_rlnMicrographName"].str.contains(m)].index , 0,inplace=True)    
+    purgedparticles.drop(purgedparticles[purgedparticles["_rlnMicrographName"].str.contains(m)].index , axis=0,inplace=True)    
     return(purgedparticles)
 
 """
@@ -122,7 +122,7 @@ def extractparticles(particles, columns, query, queryexact):
     if not queryexact:
         extractedparticles = particles.copy()
         q = "|".join(query)
-        extractedparticles.drop(extractedparticles[~extractedparticles[columns[0]].str.contains(q)].index, 0,inplace=True)
+        extractedparticles.drop(extractedparticles[~extractedparticles[columns[0]].str.contains(q)].index, axis=0,inplace=True)
     else:
         toconcat = [particles[particles[columns[0]] == q] for q in query]
         extractedparticles = pd.concat(toconcat)
@@ -212,11 +212,11 @@ def regroup(particles, numpergroup):
     regroupedparticles.sort_values("_rlnDefocusU", inplace=True)
 
     if "_rlnGroupNumber" in regroupedparticles.columns:
-        regroupedparticles.drop("_rlnGroupNumber", 1, inplace=True)
+        regroupedparticles.drop("_rlnGroupNumber", axis=1, inplace=True)
         regroupedparticles["_rlnGroupNumber"] = newgroups
 
     if "_rlnGroupName" in regroupedparticles.columns:
-        regroupedparticles.drop("_rlnGroupName", 1, inplace=True)
+        regroupedparticles.drop("_rlnGroupName", axis=1, inplace=True)
         newgroups = [("group_"+str(i).zfill(4)) for i in newgroups]
         regroupedparticles["_rlnGroupName"] = newgroups
 
@@ -331,7 +331,7 @@ def expandoptics(original_particles, original_metadata, newdata, newdata_metadat
     newoptics=newoptics.loc[newoptics.index.repeat(newoptics.times)].reset_index(drop=True)
 
     newoptics["_rlnOpticsGroup"] = range(1,totalimportoptics+len(opticsgrouplist))
-    newoptics.drop("times",1, inplace=True)
+    newoptics.drop("times",axis=1, inplace=True)
 
     newopticsnames = newoptics["_rlnOpticsGroupName"].tolist()
 

starparser/specialparticles.py

@@ -138,8 +138,8 @@ def findnearby(coreparticles,nearparticles,threshdist):
     print("\n>> Out of " + str(len(coreparticles.index)) + ", the subsets have:\n-FAR: " + str(len(farparticles.index)) + " particles\n-CLOSE: " + str(len(closeparticles.index)) + " particles\n-NO-MATCH: " + str(len(noparts)) + " particles\n")
 
     #We can remove the new column we made above before returning the dataframes
-    closeparticles.drop("_rlnMicrographNameSimple", 1, inplace=True)
-    farparticles.drop("_rlnMicrographNameSimple", 1, inplace=True)
+    closeparticles.drop("_rlnMicrographNameSimple", axis=1, inplace=True)
+    farparticles.drop("_rlnMicrographNameSimple", axis=1, inplace=True)
 
     return(farparticles, closeparticles, alldistances)
 
@@ -253,10 +253,10 @@ def getcluster(particles,threshold,minimum):
                 keep.append(names[i])
 
     if len(keep) == 0:
-        print("\n>> Error: no particles were retained based on the criteria.\n")
+        print(">> Error: no particles were retained based on the criteria.\n")
         sys.exit()
     elif len(keep) == len(particles.index):
-        print("\n>> Error: all particles were retained. No star file will be output.\n")
+        print(">> Error: all particles were retained. No star file will be output.\n")
         sys.exit()
 
     """