Introduce DICOM nodes from readdicom project

Author: Daniel Borup

fileIO/GPI/DICOMheader_GPI.py

@@ -0,0 +1,392 @@
+# Author: Ryan Robison
+# Date: 2018 Sept 14
+
+import os
+import time
+import gpi
+from gpi import QtWidgets, QtGui, QtCore
+import numpy as np
+
+# WIDGETS
+class TextBoxes(gpi.GenericWidgetGroup):
+    """A set of non-editable text boxes"""
+    valueChanged = gpi.Signal()
+
+    def __init__(self, title, parent=None):
+        super(TextBoxes, self).__init__(title, parent)
+
+        # at least one text box
+        self.boxes = []
+        self.boxes.append(QtWidgets.QLabel())
+        self.vbox = QtWidgets.QVBoxLayout()
+        self.vbox.setSpacing(0)
+        for box in self.boxes:
+            self.vbox.addWidget(box)
+        self.setLayout(self.vbox)
+
+    # setters
+    def set_strings(self, strlist):
+        """str | Set the string (str)."""
+        ind = 0
+        if len(strlist) < len(self.boxes):
+            strlendiff = len(self.boxes) - len(strlist)
+            strlist.extend(strlendiff*[''])
+            self.log.warn("TextBoxes: list of strings shorter than number of "\
+                "boxes. Filling rest with empty strings.")
+
+        if len(strlist) > len(self.boxes):
+            self.log.warn("TextBoxes: list of strings longer than number of "\
+                "boxes. Only using first portion of strings.")
+
+        for box in self.boxes:
+            string = strlist[ind]
+            box.setText(string)
+            ind = ind+1
+
+    def set_length(self, length):
+        # add specified number of text boxes
+        while length > len(self.boxes):
+            newbox = QtWidgets.QLabel()
+            self.boxes.append(newbox)
+            self.vbox.addWidget(newbox)
+        while length < len(self.boxes):
+            oldbox = self.boxes.pop()
+            oldbox.setParent(None)
+
+        if length != len(self.boxes):
+            log.critical("StringBoxes: length not properly set!")
+
+
+class StringBoxes(gpi.GenericWidgetGroup):
+    """A set of editable string boxes"""
+    valueChanged = gpi.Signal()
+
+    def __init__(self, title, parent=None):
+        super(StringBoxes, self).__init__(title, parent)
+
+        # at least one string box
+        self.boxes = []
+        self.boxes.append(QtWidgets.QLineEdit())
+        self.vbox = QtWidgets.QVBoxLayout()
+        self.vbox.setSpacing(0)
+        for box in self.boxes:
+            self.vbox.addWidget(box)
+            box.returnPressed.connect(self.valueChanged)
+        self.setLayout(self.vbox)
+
+    # setters
+    def set_strings(self, strlist):
+        """str | Set the string (str)."""
+        ind = 0
+        if len(strlist) < len(self.boxes):
+            strlendiff = len(self.boxes) - len(strlist)
+            strlist.extend(strlendiff*[''])
+            log.warn("StringBoxes: list of strings shorter than number of \
+                boxes. Filling rest with empty strings.")
+
+        if len(strlist) > len(self.boxes):
+            log.warn("StringBoxes: list of strings longer than number of \
+                boxes. Only using first portion of strings.")
+
+        for box in self.boxes:
+            string = strlist[ind]
+            box.setText(string)
+            ind = ind+1
+
+    def set_length(self, length):
+        # add specified number of string boxes
+        while length > len(self.boxes):
+            newbox = QtWidgets.QLineEdit()
+            self.boxes.append(newbox)
+            newbox.returnPressed.connect(self.valueChanged)
+            self.vbox.addWidget(newbox)
+        while length < len(self.boxes):
+            oldbox = self.boxes.pop()
+            oldbox.setParent(None)
+
+        if length != len(self.boxes):
+            log.critical("StringBoxes: length not properly set!")
+
+    def get_strings(self):
+        strings = []
+        for box in self.boxes:
+            strings.append(box.text())
+        return strings
+
+
+class DICOM_HDR_GROUP(gpi.GenericWidgetGroup):
+    """A combination of Textboxes and StringBoxes to allow for easy display of
+    DICOM header info and editing of the values"""
+    valueChanged = gpi.Signal()
+
+    def __init__(self, title, parent=None):
+        super(DICOM_HDR_GROUP, self).__init__(title, parent)
+        self._val = {}
+        self._val['tags'] = ''
+        self._val['desc'] = ''
+        self._val['VRs'] = ''
+        self._val['values'] = ''
+
+        self.tb1 = TextBoxes('Tags:')
+        self.tb1.set_length(1)
+        self.tb2 = TextBoxes('Descriptions:')
+        self.tb2.set_length(1)
+        self.tb3 = TextBoxes('VRs:')
+        self.tb3.set_length(1)
+
+        self.sb = StringBoxes('Values:')
+        self.sb.set_length(1)
+        self.sb.valueChanged.connect(self.valueChanged)
+
+        vbox = QtWidgets.QHBoxLayout()
+        vbox.addWidget(self.tb1)
+        vbox.addWidget(self.tb2)
+        vbox.addWidget(self.tb3)
+        vbox.addWidget(self.sb)
+        vbox.setStretch(0, 0)
+        vbox.setStretch(1, 0)
+        vbox.setStretch(2, 0)
+        vbox.setStretch(3, 0)
+        vbox.setContentsMargins(0, 0, 0, 0)  # we don't need margins here
+        vbox.setSpacing(0)
+        self.setLayout(vbox)
+
+    # setters
+    def set_info(self, val):
+        """A python-dict containing: tags, desc, and VRs parms. """
+        if 'tags' in val:
+            self._val['tags'] = val['tags']
+            self.setTagsQuietly(val['tags'])
+        if 'desc' in val:
+            self._val['desc'] = val['desc']
+            self.setDescriptionsQuietly(val['desc'])
+        if 'VRs' in val:
+            self._val['VRs'] = val['VRs']
+            self.setVRsQuietly(val['VRs'])
+        if 'values' in val:
+            self._val['values'] = val['values']
+            self.setValuesQuietly(val['values'])
+
+    def set_length(self, length):
+        self.tb1.set_length(length)
+        self.tb2.set_length(length)
+        self.tb3.set_length(length)
+        self.sb.set_length(length)
+
+    # getters
+    def get_val(self):
+        return self.sb.get_strings()
+
+    # support
+    def setTagsQuietly(self, val):
+        self.tb1.blockSignals(True)
+        self.tb1.set_strings(val)
+        self.tb1.blockSignals(False)
+
+    def setDescriptionsQuietly(self, val):
+        self.tb2.blockSignals(True)
+        self.tb2.set_strings(val)
+        self.tb2.blockSignals(False)
+
+    def setVRsQuietly(self, val):
+        self.tb3.blockSignals(True)
+        self.tb3.set_strings(val)
+        self.tb3.blockSignals(False)
+
+    def setValuesQuietly(self, val):
+        self.sb.blockSignals(True)
+        self.sb.set_strings(val)
+        self.sb.blockSignals(False)
+
+
+class ExternalNode(gpi.NodeAPI):
+    """This node takes in a dictionary of DICOM hdr info from ReadDICOM,
+    displays the values for the selected image, and optionally allows for
+    editing the header values. An edited DICOM header can be passed as an
+    input to WriteDICOM.
+
+    INPUT: GPI DICOM dictionary
+    OUTPUT: Modified DICOM dictionary
+
+    WIDGETS:
+    Display By - choose whether to display all hdr information for one image or
+    a single tag across all images
+    Select Image - select image for which the header will be displayed
+    Select Tag - select which Tag to display for all images
+    Propogate Change to All Images - choose whether to propogate changes to
+        DICOM header values to all image headers in the GPI DICOM dictionary.
+    Dicom Header - header information for one image (or all images, one tag).
+        The header contains the following information for each entry:
+        1) Tag - the unique tag for each header entry, hexidecimal in format,
+                 comprised of a DICOM group number and DICOM element number.
+        2) Description - A short description of each entry
+        3) VR - The DICOM value representation describing the format and type
+                of each entry.
+        4) Value - the current value of the entry. This is the only field that
+                   is editable using DICOMheader.
+    """
+
+    def execType(self):
+        # default executable type
+        # return gpi.GPI_THREAD
+        return gpi.GPI_PROCESS # this is the safest
+        # return gpi.GPI_APPLOOP
+
+    def initUI(self):
+
+        # Widgets
+        self.addWidget('ExclusivePushButtons', 'Display By', buttons=['Image','Tag'],val=0)
+        self.addWidget('ComboBox', 'Select Image', items=[])
+        self.addWidget('ComboBox', 'Select Tag', items=[])
+        self.addWidget('PushButton', 'Reset', toggle=False)
+        self.addWidget('PushButton', 'Propogate Change to All Images', toggle=False)
+        self.addWidget('DICOM_HDR_GROUP', 'Dicom Header')
+
+        # IO Ports
+        self.addInPort(title='Dicom Dict In', type='DICT')
+        self.addOutPort(title='Dicom Dict Out', type='DICT')
+
+    def validate(self):
+        import gpi_core.fileIO.dicomlib as dcm
+        import imp
+        imp.reload(dcm)
+
+        if (('Display By' in self.widgetEvents()) or
+            ('Dicom Dict In' in self.portEvents())):
+            hdr = self.getData('Dicom Dict In')
+            displayBy = self.getVal('Display By')
+            if displayBy == 0:
+                keys = list(hdr.keys())
+                numvals = len(list(hdr[keys[0]].keys()))
+                self.setAttr('Select Image', items=keys, visible=True)
+                self.setAttr('Select Tag', visible=False)
+                # self.setAttr('Images:', visible=False)
+                # self.setAttr('Tags:', visible=True)
+            else:
+                keys = list(hdr[list(hdr.keys())[0]].keys())
+                numvals = len(hdr.keys())
+                self.setAttr('Select Image', visible=False)
+                self.setAttr('Select Tag', items=keys, visible=True)
+                # self.setAttr('Images:', visible=True)
+                # self.setAttr('Tags:', visible=False)
+            self.setAttr('Dicom Header', length = numvals)
+
+
+    def compute(self):
+
+        import numpy as np
+        import re
+        import gpi_core.fileIO.dicomlib as dcm
+
+        hdr = self.getData('Dicom Dict In')
+        displayBy = self.getVal('Display By')
+        reset = self.getVal('Reset')
+        propogate = self.getVal('Propogate Change to All Images')
+
+        if ((reset) or ('Dicom Dict In' in self.portEvents())):
+            dicomDict = hdr
+        else:
+            dicomDict = self.getData('Dicom Dict Out')
+            if (dicomDict == None):
+                dicomDict = hdr
+
+        if ((reset) or ('Dicom Dict In' in self.portEvents()) or
+            ('Display By' in self.widgetEvents()) or
+            ('Select Image' in self.widgetEvents()) or
+            ('Select Tag' in self.widgetEvents())):
+            if displayBy == 0:
+                tags = []
+                descs = []
+                VRs = []
+                values = []
+                img = self.getVal('Select Image')
+                info = dicomDict[img]
+                for key in info.keys():
+                    desc = info[key][0]
+                    VR = info[key][1]
+                    val = info[key][2]
+                    tags.append(str(key))
+                    descs.append(desc)
+                    VRs.append(VR)
+                    if VR != 'SQ':
+                        values.append(val)
+                    else:
+                        values.append(str(val))
+                    # if VR == 'SQ':
+                    #     for item in val:
+                    #         for key1 in item.keys():
+                    #             desc1 = item[key1][0]
+                    #             VR1 = item[key1][1]
+                    #             val1 = item[key1][2]
+                    #             tags.append('  '+str(key1))
+                    #             descs.append(desc1)
+                    #             VRs.append(VR1)
+                    #             values.append(val1)
+                val = {'tags': tags, 'desc': descs, 'VRs': VRs, 'values': values}
+                self.setAttr('Dicom Header', info=val)
+
+            else:
+                imgs = []
+                descs = []
+                VRs = []
+                values = []
+                tag = self.getVal('Select Tag')
+                for key in dicomDict.keys():
+                    desc = dicomDict[key][tag][0]
+                    VR = dicomDict[key][tag][1]
+                    val = dicomDict[key][tag][2]
+                    imgs.append(str(key))
+                    descs.append(desc)
+                    VRs.append(VR)
+                    values.append(val)
+                val = {'tags': imgs, 'desc': descs, 'VRs': VRs, 'values': values}
+                self.setAttr('Dicom Header', info=val)
+
+        if ('Dicom Header' in self.widgetEvents()):
+            newInfo = self.getVal('Dicom Header')
+            index = 0
+            if displayBy == 0:
+                img = self.getVal('Select Image')
+                info = hdr[img]
+                for key in info.keys():
+                    val = info[key][2]
+                    newval = newInfo[index]
+                    info[key][2] = newval
+                    index = index + 1
+                dicomDict[img] = info
+            else:
+                tag = self.getVal('Select Tag')
+                for key in hdr.keys():
+                    val = hdr[key][tag][2]
+                    newval = newInfo[index]
+                    dicomDict[key][tag][2] = newval
+                    index = index + 1
+
+        if ('Propogate Change to All Images' in self.widgetEvents()):
+            if displayBy == 0:
+                curimg = self.getVal('Select Image')
+                for tag in hdr[curimg].keys():
+                    oldval = hdr[curimg][tag][2]
+                    newval = dicomDict[curimg][tag][2]
+                    if (oldval != newval):
+                        for img in hdr.keys():
+                            dicomDict[img][tag][2] = newval
+            else:
+                tag = self.getVal('Select Tag')
+                for img in hdr.keys():  # find the first changed value
+                    oldval = hdr[img][tag][2]
+                    curval = dicomDict[img][tag][2]
+                    if (oldval != curval):
+                        # update all entries in the header table
+                        values = len(hdr.keys())*[curval]
+                        val = {'values':values}
+                        self.setAttr('Dicom Header', info=val)
+                        break
+                # now update the dicom header dictionary
+                newval = self.getVal('Dicom Header')[0]
+                for img in hdr.keys():
+                    dicomDict[img][tag][2] = newval
+
+        self.setData('Dicom Dict Out', dicomDict)
+
+        return(0)