Merge branch 'master' of https://github.com/FNNDSC/pl-pfdicom_tagExtract

dcm_tagExtract/dcm_tagExtract.py

@@ -245,12 +245,24 @@ def define_parameters(self):
                             dest        = 'fileFilter',
                             optional    = True,
                             default     = '')
+        self.add_argument("--fileFilterLogic",
+                            help        = "the logic to apply across the file filter",
+                            optional    = True,
+                            type        = str,
+                            dest        = 'fileFilterLogic',
+                            default     = 'OR')
         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       = '')
+                            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("--dirFilterLogic",
+                            help        = "the logic to apply across the dir filter",
+                            dest        = 'dirFilterLogic',
+                            optional    = True,
+                            type        = str,
+                            default     = 'OR')
         self.add_argument("-F", "--tagFile",
                             help        = "file containing tags to parse",
                             type        = str,
@@ -275,6 +287,14 @@ def define_parameters(self):
                             dest        = 'imageFile',
                             optional    = True,
                             default     = '')
+        self.add_argument("--syslog",
+                            help        = "show outputs in syslog style",
+                            dest        = 'syslog',
+                            action      = 'store_true',
+                            optional    = True,
+                            type        = bool,
+                            default     = False)
+
         self.add_argument("-s", "--imageScale",
                             help        = "scale images with factor and optional :interpolation",
                             type        = str,
@@ -353,31 +373,17 @@ 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())
-        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))
+        options.str_desc = ""
+
+        # Output the space of CLI
+        d_options = vars(options)
+        for k, v in d_options.items():
+            print("%20s: %-40s" % (k, v))
+        print("")
+
+        pf_dicom_tagExtract = pfdicom_tagExtract.pfdicom_tagExtract(d_options)
         if options.version:
             print('Plugin Version: %s' % Dcm_tagExtract.VERSION)
             print('Internal pfdicom_tagExtract Version: %s' % pf_dicom_tagExtract.str_version)

requirements.txt

@@ -1,24 +1,5 @@
 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
+pftree>=3.2.32
+pfdicom>=2.0.12
+pfdicom_tagExtract>=3.1.0