Fixed import errors and requirements

dcm_tagExtract/dcm_tagExtract.py

@@ -11,7 +11,7 @@
 from chrisapp.base import ChrisApp
 
 # import the pfdicom_tagExtract module
-import  pfdicom_tagExtract
+from pfdicom_tagExtract import  pfdicom_tagExtract
 import  pudb
 import  sys
 import os
@@ -239,12 +239,18 @@ def define_parameters(self):
                             dest        = 'inputFile',
                             optional    = True,
                             default     = '')
-        self.add_argument("-e", "--extension",
+        self.add_argument("-e", "--fileFilter",
                             help        = "DICOM file extension",
                             type        = str,
-                            dest        = 'extension',
+                            dest        = 'fileFilter',
                             optional    = True,
                             default     = '')
+        self.add_argument("-d", "--dirFilter",
+                          help          = "a list of comma separated string filters to apply across the input dir space",
+                          type          = str,
+                          dest          = 'dirFilter',
+                          optional      = True,
+                          default       = '')
         self.add_argument("-F", "--tagFile",
                             help        = "file containing tags to parse",
                             type        = str,
@@ -277,7 +283,7 @@ def define_parameters(self):
                             default     = '')
         self.add_argument("-o", "--outputFileStem",
                             help        = "output file",
-                            optional    = False,
+                            optional    = True,
                             type        = str,
                             default     = "",
                             dest        = 'outputFileStem')
@@ -347,27 +353,31 @@ def run(self, options):
         """
         Define the code to be run by this plugin app.
         """
+        #args = parserDS.parse_args()
         print(Gstr_title)
         print('Version: %s' % self.get_version())
-        pf_dicom_tagExtract = pfdicom_tagExtract.pfdicom_tagExtract(
-                        inputDir            = options.inputdir,
-                        inputFile           = options.inputFile,
-                        extension           = options.extension,
-                        outputDir           = options.outputdir,
-                        outputFileStem      = options.outputFileStem,
-                        outputLeafDir       = options.outputLeafDir,
-                        useIndexhtml        = options.useIndexhtml,
-                        outputFileType      = options.outputFileType,
-                        tagFile             = options.tagFile,
-                        tagList             = options.tagList,
-                        printToScreen       = options.printToScreen,
-                        threads             = options.threads,
-                        imageFile           = options.imageFile,
-                        imageScale          = options.imageScale,
-                        verbosity           = options.verbosity,
-                        followLinks         = options.followLinks,
-                        json                = options.jsonReturn   
-                    )
+        options.str_desc = Gstr_synopsis
+        options.syslog = ""
+        # pf_dicom_tagExtract = pfdicom_tagExtract.pfdicom_tagExtract(
+        #                 inputDir            = options.inputdir,
+        #                 inputFile           = options.inputFile,
+        #                 extension           = options.extension,
+        #                 outputDir           = options.outputdir,
+        #                 outputFileStem      = options.outputFileStem,
+        #                 outputLeafDir       = options.outputLeafDir,
+        #                 useIndexhtml        = options.useIndexhtml,
+        #                 outputFileType      = options.outputFileType,
+        #                 tagFile             = options.tagFile,
+        #                 tagList             = options.tagList,
+        #                 printToScreen       = options.printToScreen,
+        #                 threads             = options.threads,
+        #                 imageFile           = options.imageFile,
+        #                 imageScale          = options.imageScale,
+        #                 verbosity           = options.verbosity,
+        #                 followLinks         = options.followLinks,
+        #                 json                = options.jsonReturn
+        #             )
+        pf_dicom_tagExtract = pfdicom_tagExtract.pfdicom_tagExtract(vars(options))
         if options.version:
             print('Plugin Version: %s' % Dcm_tagExtract.VERSION)
             print('Internal pfdicom_tagExtract Version: %s' % pf_dicom_tagExtract.str_version)

requirements.txt

@@ -1,4 +1,24 @@
-chrisapp~=2.4.0
-nose~=1.3.7
-pillow
-pfdicom_tagExtract~=3.1.0
+chrisapp==2.4.0
+cycler==0.10.0
+Faker==9.3.1
+jedi==0.18.0
+kiwisolver==1.3.2
+matplotlib==3.4.3
+nose==1.3.7
+numpy==1.21.2
+parso==0.8.2
+pfdicom==2.0.12
+pfdicom-tagExtract==3.1.0
+pfmisc==2.2.8
+pftree==3.4.2
+Pillow==8.4.0
+pudb==2021.1
+pydicom==2.2.2
+pydicom-ext==0.6.1
+Pygments==2.10.0
+pyparsing==2.4.7
+python-dateutil==2.8.2
+six==1.16.0
+text-unidecode==1.3
+urwid==2.1.2
+

setup.py

@@ -6,7 +6,7 @@
 
 setup(
     name             = 'dcm_tagExtract',
-    version          = '3.2.0',
+    version          = '3.2.1',
     description      = 'This app performs a recursive walk down an input tree, and for each location with a DICOM file, will generate a report in the corresponding location in the output tree.',
     long_description = readme,
     author           = 'Sandip Samal',