在Python中使用rpy2軟件包：Rruntime錯誤未被用戶代碼處理

Question

我正嘗試在使用rpy2軟件包的python中創建一個r環境。我試圖創建一個我從圖像中提取的ROI的GLRLM。我在加載軟件包時遇到了一些問題，但我終於設法做到了。現在我在運行代碼時出現以下錯誤：

RuntimeError was unhandled by user code

在這一行：

ro.r('glrlmatrix <- radiomics:::glrlm(tissue)')

我懷疑它無法找到函數「glrlm」。我試着運行R中的代碼，它工作正常。任何人都知道該怎麼做？

tissue = pd.DataFrame(rgbRoi[...,0]) 
rdf= pandas2ri.py2ri(tissue) 
ro.globalenv['tissue'] = rdf 
radiomics=importr("radiomics",lib_loc="C:/Users/nka/Documents/R/win-library/3.3"); 
ro.r('tissue <- as.matrix(tissue)') 
ro.r('print(dim(tissue))') 
ro.r('library(radiomics)') 
ro.r('glrlmatrix <- radiomics:::glrlm(tissue)') 
ro.r('glrlmatrix[0,] <- 0')       ### Assign zero value to first row which belongs to mask region 
ro.r('glrlfeature  <- array(NA,dim=c(11,1))') 
ro.r('glrlfeature[1,1] <- radiomics:::glrlm_GLN(glrlmatrix)') 
ro.r('glrlfeature[2,1] <- radiomics:::glrlm_HGLRE(glrlmatrix)') 
ro.r('glrlfeature[3,1] <- radiomics:::glrlm_LRE(glrlmatrix)') 
ro.r('glrlfeature[4,1] <- radiomics:::glrlm_LRHGLE(glrlmatrix)') 
ro.r('glrlfeature[5,1] <- radiomics:::glrlm_LRLGLE(glrlmatrix)') 
ro.r('glrlfeature[6,1] <- radiomics:::glrlm_LGLRE(glrlmatrix)') 
ro.r('glrlfeature[7,1] <- radiomics:::glrlm_RLN(glrlmatrix)') 
ro.r('glrlfeature[8,1] <- radiomics:::glrlm_RP(glrlmatrix)') 
ro.r('glrlfeature[9,1] <- radiomics:::glrlm_SRE(glrlmatrix)') 
ro.r('glrlfeature[10,1] <- radiomics:::glrlm_SRHGLE(glrlmatrix)') 
ro.r('glrlfeature[11,1] <- radiomics:::glrlm_SRLGLE(glrlmatrix)') 
glr = ro.r.matrix(ro.r('glrlfeature')) 
glr = np.array(glr) 

Answer 1

在做radiomics:::glrlm您正在訪問的符號glrlm在命名空間radiomics而無法導出它（使用::只訪問導出的符號）。這應該在R中工作，並用ro.r解析/評估R字符串。但是，符號通常不會被R包導出，因爲它們並不意味着被普通用戶直接訪問。

另外消息RuntimeError was unhandled by user code似乎不是來自rpy2。這真的是所有報告有關錯誤？

在這旁邊，你可能會考慮遷移一些將R串到Python 的（如果你認爲這是與可讀性幫助）：

# this is implicitly loading the R package 
radiomics=importr("radiomics", 
        lib_loc="C:/Users/nka/Documents/R/win-library/3.3"); 
# the line below is then unnecessary because of the above 
# ro.r('library(radiomics)') 

# binding the symbol "tissue" in R's globalenv to the matrix conversion 
# of the data frame of the same name can be written more like Python 
# code: 
base = importr("base") 
tissue_mat = base.as_matrix(tissue) 
ro.globalenv['tissue'] = tissue_mat 
# the following should work, unless the R code in `radiomics::glrlm` 
# cannot handle anonymous objects 
glrlmatrix = radiomics.glrlm(tissue_mat) 
# glrmatrix is a Python/rpy2 objects that also be used as a numpy array 
# and modified in-place 
# (see http://rpy2.readthedocs.io/en/version_2.8.x/numpy.html#from-rpy2-to-numpy)