Specify min dependency and minor cleanups.

colonycounter.py

@@ -122,7 +122,6 @@ def main():
         [f.opqueue.__init__([normalize, to8bit, rollingball, wat]) for f in files]
         [f.apply(dslice(f.opqueue,None,-1)) for f in files]
 
-        # [(f.apply(f.opqueue), f.save(True, f.opqueue)) for f in files]
         window.init(files)
         window.reset()
         return True

fileutils.py

@@ -53,7 +53,7 @@ class FILE:
                     self.meta = pd.DataFrame(None if self.data[1]["data"][1:] == [] else self.data[1]["data"][1:], columns=self.data[1]["data"][0])
                     self.meta.insert(loc=0, column="Label", value="".join([self.fname, self.fext]))
                     spath = self.path.split(path.sep)
-                    if len(spath) > 2 and spath[-1] in ["BFP", "YFP"] and spath[-2][:-1].isdigit():
+                    if len(spath) > 2 and spath[-2][:-1].isdigit():
                         hour, culture = self.path.split(path.sep)[-2:]
                         hour = int(hour[:-1])
                     else:
@@ -82,11 +82,7 @@ class FILE:
             if self.outlines is not None:
                 imwrite(path.join(DIROUT, self.path, f"{self.fname}.outlines.jpg"), self.outlines)
             if self.meta is not None:
-                print(path.join(DIROUT, self.path, f"{self.fname}.csv"))
                 self.meta.to_csv(path.join(DIROUT, self.path, f"{self.fname}.csv"), index=False)
-                # [l.insert(1, self.getName(False, {})) for l in self.meta["data"][1:]]
-                # with open(path.join(DIROUT, self.path, f"{self.fname}.csv"), "w") as f:
-                #     [f.write(",".join([str(e) for e in l]) + "\n") for l in self.meta["data"]]
         else:
             if not path.exists(path.join(DIRCACHE, self.path)):
                 makedirs(path.join(DIRCACHE, self.path))

requirements.txt

@@ -1,5 +1,5 @@
 numpy
 opencv-python == 4.3.0
 pythreshold
-scikit-image
+scikit-image >= 0.18.1
 scipy