Merge pull request #138 from friskluft/POL3369_fixed_featurize_files

POL3369 Python API changes: [1] fixed featurize_files(); [2] control of verbosity level

README.md

@@ -57,7 +57,8 @@ features = nyx.featurize_files(
         "/path/to/images/labels/m1.ome.tif", 
         "/path/to/images/labels/m2.ome.tif",
         "/path/to/images/labels/m2.ome.tif"
-    ])
+    ],
+	False)
 ```
 
 The `features` variable is a Pandas dataframe similar to what is shown below.

src/nyx/environment.cpp

@@ -727,7 +727,7 @@ bool Environment::parse_cmdline(int argc, char **argv)
 				find_string_argument(i, GLCMANGLES, rawGlcmAngles) ||
 				find_string_argument(i, PXLDIST, pixel_distance) ||
 				find_string_argument(i, COARSEGRAYDEPTH, raw_coarse_grayscale_depth) ||
-				find_string_argument(i, VERBOSITY, verbosity) ||
+				find_string_argument(i, VERBOSITY, rawVerbosity) ||
 				find_string_argument(i, IBSICOMPLIANCE, raw_ibsi_compliance) ||
 				find_string_argument(i, RAMLIMIT, rawRamLimit) ||
 				find_string_argument(i, TEMPDIR, rawTempDir) ||
@@ -918,10 +918,10 @@ bool Environment::parse_cmdline(int argc, char **argv)
 		}
 	}
 
-	if (!verbosity.empty())
+	if (!rawVerbosity.empty())
 	{
 		// string -> integer
-		if (sscanf(verbosity.c_str(), "%d", &verbosity_level) != 1 || verbosity_level < 0)
+		if (sscanf(rawVerbosity.c_str(), "%d", &verbosity_level) != 1 || verbosity_level < 0)
 		{
 			std::cout << "Error: " << VERBOSITY << "=" << reduce_threads << ": expecting a positive integer constant\n";
 			return false;

src/nyx/environment.h

@@ -143,7 +143,7 @@ class Environment: public BasicEnvironment
 	std::string rawGlcmAngles = "";
 	std::vector<int> glcmAngles = {0, 45, 90, 135};
 
-	std::string verbosity = "";	// 'verbosity_level' is inherited from BasicEnvironment
+	std::string rawVerbosity = "";	// 'verbosity_level' is inherited from BasicEnvironment
 
 	std::string rawOnlineStatsThresh = "";
 	int onlineStatsTreshold = 0;

src/nyx/python/new_bindings_py.cpp

@@ -106,7 +106,7 @@ void set_environment_params_imp (
     uint32_t n_reduce_threads = 0,
     uint32_t n_loader_threads = 0,
     int using_gpu = -2,
-    int verbosity_level = 0
+    int verb_level = 0
 ) {
     if (features.size() > 0) {
         theEnvironment.recognizedFeatureNames = features;
@@ -132,8 +132,10 @@ void set_environment_params_imp (
         theEnvironment.n_loader_threads = n_loader_threads;
     }
 
-    if (verbosity_level != 0)
-        theEnvironment.verbosity = verbosity_level;
+    if (verb_level >= 0)
+        theEnvironment.set_verbosity_level (verb_level);
+    else
+        throw std::runtime_error("Error: verbosity (" + std::to_string(verb_level) + ") should be a non-negative value");
 }
 
 py::tuple featurize_directory_imp (
@@ -289,10 +291,10 @@ py::tuple featurize_montage_imp (
     return py::make_tuple(error_message);
 }
 
-py::tuple featurize_fname_lists_imp (const py::list& int_fnames, const py::list & seg_fnames, bool pandas_output=true)
+py::tuple featurize_fname_lists_imp (const py::list& int_fnames, const py::list & seg_fnames, bool single_roi, bool pandas_output=true)
 {
     // Set the whole-slide/multi-ROI flag
-    theEnvironment.singleROI = false;
+    theEnvironment.singleROI = single_roi;
 
     std::vector<std::string> intensFiles, labelFiles;
     for (auto it = int_fnames.begin(); it != int_fnames.end(); ++it)
@@ -363,7 +365,6 @@ py::tuple featurize_fname_lists_imp (const py::list& int_fnames, const py::list
             pyNumData = pyNumData.reshape({ nRows, pyNumData.size() / nRows });
 
             return py::make_tuple(pyHeader, pyStrData, pyNumData);
-
     } 
 
     // Return "nothing" when output will be an Arrow format

src/nyx/python/nyxus/nyxus.py

@@ -388,18 +388,20 @@ def featurize_files (
         self,
         intensity_files: list,
         mask_files: list,
+        single_roi: bool,
         output_type: Optional[str] = "pandas",
         output_path: Optional[str] = ""):
         """Extract features from image file pairs passed as lists
 
         Extracts all the requested features _at the image level_ from the intensity images
         present in list `intensity_files` with respect to region of interest masks presented in 
-        list `mask_files`. Multiple 
+        list `mask_files`. Single-ROI feature extraction is enforced via passing 'True' as parameter 'single_roi'
 
         Parameters
         ----------
         intensity_files : list of intensity image file paths
         mask_files : list of mask image file paths
+        single_roi : 'True' to treat items of 'intensity_files' as single-ROI ('mask_files' will be ignored), 'False' to treat items of 'intensity_files' and 'mask_files' as intensity/segmentation image pairs
 
         Returns
         -------
@@ -415,11 +417,11 @@ def featurize_files (
             raise IOError ("The list of segment file paths is empty")
 
         if (output_type not in self._valid_output_types):
-            raise  ValueError(f'Invalid output type {output_type}. Valid output types are {self._valid_output_types}.')
+            raise  ValueError(f'Invalid output type {output_type}. Valid output types are {self._valid_output_types}')
 
         if (output_type == 'pandas'):
 
-            header, string_data, numeric_data = featurize_fname_lists_imp (intensity_files, mask_files, True)
+            header, string_data, numeric_data = featurize_fname_lists_imp (intensity_files, mask_files, single_roi, True)
 
             df = pd.concat(
                 [
@@ -437,7 +439,7 @@ def featurize_files (
 
         else:
 
-            featurize_fname_lists_imp (intensity_files, mask_files, False)
+            featurize_fname_lists_imp (intensity_files, mask_files, single_roi, False)
 
             output_type = output_type.lower() # ignore case of output type
 
@@ -579,6 +581,8 @@ def set_environment_params (self, **params):
             Id of the gpu to use. To find available gpus along with ids, using nyxus.get_gpu_properties().
             The default value of -1 uses cpu calculations. Note that the gpu features only support a single 
             thread for feature calculation. 
+        * verbose: int (optional, non-negative, default 0)
+            Level of diagnostic output shown in the console. Set '0' to disable any diagnostic output.
         
         """