immucellai2 2.1.30__py3-none-any.whl → 2.1.32__py3-none-any.whl

immucellai2/Deconvolution.py

@@ -267,36 +267,33 @@ def MainRun(RunObject, seed=42, MultithreadModule = 'joblib'):
             RunObject.SampleList[sample_index], 
             RunObject.MAPorMLE 
         )) 
-    #EmceeParameterCopy = RunObject.EmceeParameter.mycopy() 
-    MultiprocessingReturnValue = [] 
+    MultiprocessingReturnValue = []
     if MultithreadModule == 'joblib':
-        try: 
-            results = joblib.Parallel(n_jobs=int(EnvironmentRun.ThreadNum), backend='loky',verbose=0)(joblib.delayed(ThreadRunEachSamples)(*arg) for arg in parameterlist) 
-        except: 
-            print('error occurs while paralleling') 
-        finally: 
-            del parameterlist 
-            print('finished all!') 
+       try:
+          MultiprocessingReturnValue = joblib.Parallel(n_jobs=int(EnvironmentRun.ThreadNum), backend='loky',verbose=0)(joblib.delayed(ThreadRunEachSamples)(*arg) for arg in parameterlist)
+       except:
+          print('error occurs while paralleling')
+       finally:
+          del parameterlist
+          print('finished all!')
     elif MultithreadModule == 'multiprocessing':
         with multiprocessing.Pool(processes=int(EnvironmentRun.ThreadNum)) as pool:
-            results = pool.starmap(
-                ThreadRunEachSamples, 
-                [(EmceeParameterCopy, 
-                  CelltypesReferenceMatrix, 
-                  RunObject.SamplesBulkRNAseqExpression[sample_index], 
-                  RunObject.SampleList[sample_index], 
-                  seed + sample_index, 
-                  RunObject.MAPorMLE
-                  ) for sample_index in range(nsamples)]
-            )   
+            try:
+                MultiprocessingReturnValue = pool.starmap(ThreadRunEachSamples, parameterlist)
+            except Exception as e:
+                print(f'Error occurs while paralleling: {e}')
+            finally:
+                pool.close()
+                pool.join()
+                print('Finished all!')
     MergedResultObject = MergeResultsForAllSample(
-        ThreadList=[MultiprocessesResult(
-            RunObject.SampleList[i], 
-            result, 
-            deepcopy(RunObject.CellType)
-        ) for i, result in enumerate(results)],
+        ThreadList = [MultiprocessesResult(
+            SampleName = RunObject.SampleList[Sampleii],
+            SamplingResult = MultiprocessingReturnValue[Sampleii],
+            CellType=deepcopy(RunObject.CellType),
+        )   for Sampleii in range(len(MultiprocessingReturnValue))],
         OtherParams=[deepcopy(RunObject.CellType), RunObject.FileCellTypeCategory]
-    ) 
+        ) 
     RecordTime.ShowCostTime()
     if os.path.exists("TempThread"): 
         os.system("rm -rf TempThread")

immucellai2/myclasses.py

@@ -99,16 +99,10 @@ class CLASS_FOR_RUNRESULT(object):
             self.EmceeFunction2( McSamplingResultList[sampleii, :, :, :] )
       return  NewMcSamplingResultList
    def optimized_calculation(self, FlatSamplingResultOne, nCellType):
-      row_sums = FlatSamplingResultOne.sum(axis=1, keepdims=True)
-      row_sums_safe = row_sums + 1e-10 
-      if FlatSamplingResultOne.shape[1] == nCellType:
-         return FlatSamplingResultOne / row_sums_safe
-      elif FlatSamplingResultOne.shape[1] + 1 == nCellType:
-         normalized = FlatSamplingResultOne / row_sums_safe
-         last_col = 1 - normalized.sum(axis=1, keepdims=True)
-         return numpy.column_stack((normalized, last_col))
-      else:
-         raise ValueError(f"Dimension mismatch: input {FlatSamplingResultOne.shape[1]} columns, target {nCellType}columns")
+       if FlatSamplingResultOne.shape[1] == nCellType:
+           return FlatSamplingResultOne / FlatSamplingResultOne.sum(axis=1)[:, None]
+       elif FlatSamplingResultOne.shape[1] + 1 == nCellType:
+           return numpy.column_stack((FlatSamplingResultOne, 1 - FlatSamplingResultOne.sum(axis=1)))
    def EmceeFunction2(self, FlatSamplingResultList): 
       fshape = FlatSamplingResultList.shape
       nCellType = len(self.CellType)

{immucellai2-2.1.30.dist-info → immucellai2-2.1.32.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: immucellai2
-Version: 2.1.30
+Version: 2.1.32
 Summary: A tool for immune cell type deconvolution
 Home-page: https://github.com/VyvyanYjm/ImmuCellAI2.0
 Author: YangJingmin

{immucellai2-2.1.30.dist-info → immucellai2-2.1.32.dist-info}/RECORD

@@ -1,16 +1,16 @@
-immucellai2/Deconvolution.py,sha256=8fYLWKHFf1qahY7qEt5nnsrju7S7kF9f2ch3YXaKQMU,12577
+immucellai2/Deconvolution.py,sha256=Ai3cE_YhVXyu5OWymnNbRqGWUHdXiTE8FVSmu5pdNvM,12507
 immucellai2/Drawplot.py,sha256=YnUleceEyim9SsTiU18mbAMcjOH9ovBXJW3pwXxA7as,5136
 immucellai2/ObtainCategory.py,sha256=N1F_yUHoaIisnlms4aNNJ2UIzZDI2TIc0t7IRLtM7So,7008
 immucellai2/PrepareData.py,sha256=tJWtQbfFfXszAQMnAmyzFrXB40wgHl48WP3WZKfeifg,5935
 immucellai2/Time.py,sha256=et3aAqyVDKwP5_tdGIwA6yxdXRbbYemc9wEaPHpQCck,572
 immucellai2/__init__.py,sha256=wi7UznfkskCvT4yj-u1RuyN0SK1tZptpXffIaQW2XkQ,3055
-immucellai2/myclasses.py,sha256=9Rgil00HX_RfOhvpdvUZDsvFi7RdIfXay4V3lRcQsQ8,12409
+immucellai2/myclasses.py,sha256=LFVMgIwraRrw_uv4g5BG-799AiH3apHXc-mBlAlYRd4,12120
 immucellai2/myconfig/Celltype.category,sha256=l_5vspGpyDbuaQ7QOLIQjSs4xb6x6_pvvtnP709CVzQ,5530
 immucellai2/myconfig/MarkerUsedDeconvolution.txt,sha256=33gCFD1_Clis7NFaQTUHc5s7BXoN61jWgWPgjT-m0n0,60756
 immucellai2/myconfig/reference_normalCelltypes.txt,sha256=zhKP5Z1TgVyB6ijIamjM1ETmuwQgRATofO-0ds89gP4,39107049
 immucellai2/myconfig/reference_tumorCelltypes.txt,sha256=xYgjehHIXb5re20bmXeoqxfyvQmgpr4y-0ysCVnEeI8,40893156
-immucellai2-2.1.30.dist-info/METADATA,sha256=NKn592muAUBDhIluHj7pKTLUOrdpNxGwXGn64E_fpKQ,1662
-immucellai2-2.1.30.dist-info/WHEEL,sha256=wUyA8OaulRlbfwMtmQsvNngGrxQHAvkKcvRmdizlJi0,92
-immucellai2-2.1.30.dist-info/entry_points.txt,sha256=asskhaErD37JB_X_4TPB1itaIytWCU-RHFIyVGQ8Jbw,62
-immucellai2-2.1.30.dist-info/top_level.txt,sha256=9r84YbXmTdnKZnK2OGrTsgYPFoSBdk4EkeieDg-7_DY,12
-immucellai2-2.1.30.dist-info/RECORD,,
+immucellai2-2.1.32.dist-info/METADATA,sha256=w38DgKWAAk7CitVbgQCeFPrzutbR6d--KeHeRIsVhTM,1662
+immucellai2-2.1.32.dist-info/WHEEL,sha256=wUyA8OaulRlbfwMtmQsvNngGrxQHAvkKcvRmdizlJi0,92
+immucellai2-2.1.32.dist-info/entry_points.txt,sha256=asskhaErD37JB_X_4TPB1itaIytWCU-RHFIyVGQ8Jbw,62
+immucellai2-2.1.32.dist-info/top_level.txt,sha256=9r84YbXmTdnKZnK2OGrTsgYPFoSBdk4EkeieDg-7_DY,12
+immucellai2-2.1.32.dist-info/RECORD,,