melage 0.0.65__py3-none-any.whl

melage/graphics/shaders.py

@@ -0,0 +1,202 @@
+try:
+    from OpenGL import NullFunctionError
+except ImportError:
+    from OpenGL.error import NullFunctionError
+from OpenGL.GL import *
+from OpenGL.GL import shaders
+import re
+
+## For centralizing and managing vertex/fragment shader programs.
+
+def initShaders():
+    global Shaders
+    Shaders = [
+        ShaderProgram(None, []),
+        ShaderProgram('pointSprite', [   ## allows specifying point size using normal.x
+            ## See:
+            ##
+            ##  http://stackoverflow.com/questions/9609423/applying-part-of-a-texture-sprite-sheet-texture-map-to-a-point-sprite-in-ios
+            ##  http://stackoverflow.com/questions/3497068/textured-points-in-opengl-es-2-0
+            ##
+            ##
+            VertexShader("""
+                void main() {
+                    gl_FrontColor=gl_Color;
+                    gl_PointSize = gl_Normal.x;
+                    gl_Position = ftransform();
+                } 
+            """),
+        ]),
+    ]
+
+
+CompiledShaderPrograms = {}
+    
+def getShaderProgram(name):
+    return ShaderProgram.names[name]
+
+class Shader(object):
+    def __init__(self, shaderType, code):
+        self.shaderType = shaderType
+        self.code = code
+        self.compiled = None
+        
+    def shader(self):
+        if self.compiled is None:
+            try:
+                self.compiled = shaders.compileShader(self.code, self.shaderType)
+            except NullFunctionError:
+                raise Exception("This OpenGL implementation does not support shader programs; many OpenGL features in pyqtgraph will not work.")
+            except RuntimeError as exc:
+                ## Format compile errors a bit more nicely
+                if len(exc.args) == 3:
+                    err, code, typ = exc.args
+                    if not err.startswith('Shader compile failure'):
+                        raise
+                    code = code[0].decode('utf_8').split('\n')
+                    err, c, msgs = err.partition(':')
+                    err = err + '\n'
+                    msgs = re.sub('b\'','',msgs)
+                    msgs = re.sub('\'$','',msgs)
+                    msgs = re.sub('\\\\n','\n',msgs)
+                    msgs = msgs.split('\n')
+                    errNums = [()] * len(code)
+                    for i, msg in enumerate(msgs):
+                        msg = msg.strip()
+                        if msg == '':
+                            continue
+                        m = re.match(r'(\d+\:)?\d+\((\d+)\)', msg)
+                        if m is not None:
+                            line = int(m.groups()[1])
+                            errNums[line-1] = errNums[line-1] + (str(i+1),)
+                            #code[line-1] = '%d\t%s' % (i+1, code[line-1])
+                        err = err + "%d %s\n" % (i+1, msg)
+                    errNums = [','.join(n) for n in errNums]
+                    maxlen = max(map(len, errNums))
+                    code = [errNums[i] + " "*(maxlen-len(errNums[i])) + line for i, line in enumerate(code)]
+                    err = err + '\n'.join(code)
+                    raise Exception(err)
+                else:
+                    raise
+        return self.compiled
+
+class VertexShader(Shader):
+    def __init__(self, code):
+        Shader.__init__(self, GL_VERTEX_SHADER, code)
+        
+class FragmentShader(Shader):
+    def __init__(self, code):
+        Shader.__init__(self, GL_FRAGMENT_SHADER, code)
+        
+        
+        
+
+class ShaderProgram(object):
+    names = {}
+    
+    def __init__(self, name, shaders, uniforms=None):
+        self.name = name
+        ShaderProgram.names[name] = self
+        self.shaders = shaders
+        self.prog = None
+        self.blockData = {}
+        self.uniformData = {}
+        
+        ## parse extra options from the shader definition
+        if uniforms is not None:
+            for k,v in uniforms.items():
+                self[k] = v
+        
+    def setBlockData(self, blockName, data):
+        if data is None:
+            del self.blockData[blockName]
+        else:
+            self.blockData[blockName] = data
+
+    def setUniformData(self, uniformName, data):
+        if data is None:
+            del self.uniformData[uniformName]
+        else:
+            self.uniformData[uniformName] = data
+            
+    def __setitem__(self, item, val):
+        self.setUniformData(item, val)
+        
+    def __delitem__(self, item):
+        self.setUniformData(item, None)
+
+    def program(self):
+        if self.prog is None:
+            try:
+                compiled = [s.shader() for s in self.shaders]  ## compile all shaders
+                self.prog = shaders.compileProgram(*compiled)  ## compile program
+            except:
+                self.prog = -1
+                raise
+        return self.prog
+        
+    def __enter__(self):
+        if len(self.shaders) > 0 and self.program() != -1:
+            glUseProgram(self.program())
+            
+            try:
+                ## load uniform values into program
+                for uniformName, data in self.uniformData.items():
+                    loc = self.uniform(uniformName)
+                    if loc == -1:
+                        raise Exception('Could not find uniform variable "%s"' % uniformName)
+                    if type(data)==int:
+                        glUniform1i(loc, data)
+                    else:
+                        glUniform1fv(loc, len(data), data)
+                    
+                ### bind buffer data to program blocks
+                #if len(self.blockData) > 0:
+                    #bindPoint = 1
+                    #for blockName, data in self.blockData.items():
+                        ### Program should have a uniform block declared:
+                        ### 
+                        ### layout (std140) uniform blockName {
+                        ###     vec4 diffuse;
+                        ### };
+                        
+                        ### pick any-old binding point. (there are a limited number of these per-program
+                        #bindPoint = 1
+                        
+                        ### get the block index for a uniform variable in the shader
+                        #blockIndex = glGetUniformBlockIndex(self.program(), blockName)
+                        
+                        ### give the shader block a binding point
+                        #glUniformBlockBinding(self.program(), blockIndex, bindPoint)
+                        
+                        ### create a buffer
+                        #buf = glGenBuffers(1)
+                        #glBindBuffer(GL_UNIFORM_BUFFER, buf)
+                        #glBufferData(GL_UNIFORM_BUFFER, size, data, GL_DYNAMIC_DRAW)
+                        ### also possible to use glBufferSubData to fill parts of the buffer
+                        
+                        ### bind buffer to the same binding point
+                        #glBindBufferBase(GL_UNIFORM_BUFFER, bindPoint, buf)
+            except:
+                glUseProgram(0)
+                raise
+                    
+            
+        
+    def __exit__(self, *args):
+        if len(self.shaders) > 0:
+            glUseProgram(0)
+        
+    def uniform(self, name):
+        """Return the location integer for a uniform variable in this program"""
+        return glGetUniformLocation(self.program(), name.encode('utf_8'))
+
+    #def uniformBlockInfo(self, blockName):
+        #blockIndex = glGetUniformBlockIndex(self.program(), blockName)
+        #count = glGetActiveUniformBlockiv(self.program(), blockIndex, GL_UNIFORM_BLOCK_ACTIVE_UNIFORMS)
+        #indices = []
+        #for i in range(count):
+            #indices.append(glGetActiveUniformBlockiv(self.program(), blockIndex, GL_UNIFORM_BLOCK_ACTIVE_UNIFORM_INDICES))
+        
+
+initShaders()

melage/main.py

@@ -0,0 +1,270 @@
+# This Python file uses the following encoding: utf-8
+import sys
+
+import os
+sys.path.append('.')
+sys.path.append("../")
+#print(sys.path)
+from PyQt5 import QtWidgets, QtCore, QtGui
+#from PyQt5.QtWidgets import QWidget
+from melage.widgets.mainwindow_widget import Ui_Main
+from melage.widgets.activation import activation_dialog
+
+from melage.utils.source_folder import source_folder, desktop
+
+## verifyClass
+class verifyClass(QtCore.QObject):
+    sig = QtCore.pyqtSignal(int)
+    def __init__(self):
+        super().__init__()
+
+    def verify_func(self):
+        ## your verification code
+        self.sig.emit(1) ## mean the verification is okay, do it if verification success
+
+
+
+class MainWindow(QtWidgets.QMainWindow, Ui_Main):
+    def __init__(self, *args, app = None, **kwargs):
+
+
+
+        super(MainWindow, self).__init__(*args, **kwargs)
+        QtWidgets.QWidget.__init__(self)
+        self.app = app
+        self.setupUi(self)
+        if os.path.isdir(desktop):
+            self.source_dir = desktop
+        #self.settings.setPath(self.settings.IniFormat, self.settings.UserScope, '.')
+
+        self.setWindowIcon(QtGui.QIcon(source_folder+'/main.ico'))
+        self._key_picke = b'PPQ0ByoMsieWGv6bMEyJ9rSYXQDoa5D4ldAkwaNNpw0='
+
+        if not self.settings.value("geometry") == None:
+            self.restoreGeometry(self.settings.value("geometry"))
+        #QtCore.QTimer.singleShot(5000, self.showChildWindow)
+
+        self._openUSEnabled = True
+        ######################### Load connect ################################
+        self.actionLoad.triggered.connect(self.loadChanges)
+        key_needed = False
+        if key_needed:
+
+
+            self.setEnabled(False)
+            self.activation_dialog = activation_dialog(self,source_folder)
+            self.activation_dialog.correct_key.connect(self.EnableAll)
+            verifyInstance = verifyClass()
+            verifyInstance.sig.connect(self.verify_func)
+            thread = QtCore.QThread()
+            self._v_thread = (thread, verifyInstance)
+            verifyInstance.moveToThread(thread)
+            thread.started.connect(verifyInstance.verify_func)
+            thread.start()
+        else:
+            self.setEnabled(True)
+
+
+
+
+    def verify_func(self, i):
+        if i == 1:
+            if self.activation_dialog.verify():
+                self.EnableAll(self.activation_dialog.options)
+            else:
+                self.activation_dialog.exec_()
+
+
+            ## enable your buttons
+
+    def EnableAll(self, options):
+        if options=='FULL':
+            #self.menuExport.setEnabled(False)
+            #self.menuPreprocess.setEnabled(False)
+            #self.actionCircles.setEnabled(False)
+
+            '''
+            
+            self.actionPoints.setEnabled(False)
+            self.menuSeg.setEnabled(False)
+            
+            self.actionsaveModified.setVisible(False)
+            self.actionconvert.setVisible(False)
+            self.menuCalc.setEnabled(False)
+            '''
+            self._openUSEnabled = True
+            self.setEnabled(True)
+            self.menuSeg.setEnabled(False)
+            self.menuCalc.setEnabled(False)
+
+            self.menuRegistration.setEnabled(False)
+
+    def saveChanges(self):
+        from melage.utils.utils import getAttributeWidget
+        try:
+            import cPickle as pickle
+        except ModuleNotFoundError:
+            import pickle
+        from collections import defaultdict
+        from PyQt5.QtCore import QSettings
+        from time import gmtime, strftime
+        self.settings.sync()
+        dic = defaultdict(list)
+
+
+        """
+        
+        if filePath == None:
+            basefile = ''
+            if hasattr(self, 'readImECO'):
+                basefile =self.readImECO.basefile
+            if basefile == '':
+                if hasattr(self, 'readImMRI'):
+                    basefile = self.readImMRI.basefile
+        else:
+            basefile = filePath[0]
+
+        if basefile[-3:] == '.bn':
+            basefile = basefile[:-3]
+
+        self._basefileSave = basefile
+        """
+        self.settings = QSettings(self._basefileSave+ '.ini', self.settings.IniFormat)
+
+        self.progressBarSaving.setValue(10)
+        self.settings.setValue("geometry", self.saveGeometry())
+        self.settings.setValue("windowState", self.saveState())
+        self.progressBarSaving.setValue(20)
+
+
+        name = 'openGLWidget_'
+        widgets_num = [0, 1, 2, 3, 4, 5, 10, 11,13,23]
+        for i in widgets_num:
+            nameWidget = name+str(i+1)
+            if hasattr(self, name+str(i+1)):
+                widget =getattr(self, name+str(i+1))
+                dic = getAttributeWidget(widget, nameWidget, dic)
+        self.progressBarSaving.setValue(40)
+        names = ['readImECO', 'readImMRI']
+        for name in names:
+            if hasattr(self, name):
+                readD = getattr(self, name)
+                #dic[name] = {}
+                dic = getAttributeWidget(readD, name, dic)
+        table_items = []
+        rows = self.table_widget_measure.rowCount()
+        cols = self.table_widget_measure.columnCount()
+        for row in range(rows):
+            txts = []
+            for col in range(cols):
+                if hasattr(self.table_widget_measure.item(row, col),'text'):
+                    txt = self.table_widget_measure.item(row, col).text()
+                    txts.append(txt)
+            table_items.append(txts)
+        dic['measurements'] = table_items
+
+
+        self.progressBarSaving.setValue(60)
+        dic = getAttributeWidget(self, 'main', dic)
+        self.progressBarSaving.setValue(80)
+
+        dic['versionInfo'] = defaultdict(list)
+        dic['versionInfo']['__version__'] = 'Neobrain_1.0.6'
+        dic['versionInfo']['dataTime'] = strftime("%Y_%m_%d_%H%M%S", gmtime())
+
+
+ #       with open(self._basefileSave+'.bn', 'w+') as f:
+#            f.write('0\n')
+
+        self.progressBarSaving.setValue(90)
+
+
+        #fp = gzip.open('primes.data', 'wb')
+        from cryptography.fernet import Fernet
+        with open(self._basefileSave+'.bn', 'wb') as output:
+            pickle.dump(dic, output, pickle.HIGHEST_PROTOCOL)
+
+        f = Fernet(self._key_picke)
+        with open(self._basefileSave+'.bn', 'rb') as file:
+            # read all file data
+            file_data = file.read()
+        encrypted_data = f.encrypt(file_data)
+        with open(self._basefileSave+'.bn', 'wb') as file:
+            file.write(encrypted_data)
+        self.progressBarSaving.setValue(100)
+
+    def createPopupMenu(self): # overriding create popup menu
+        menu = super().createPopupMenu()
+        for action in menu.actions():
+            if action.text()=='Progress Bar':
+                menu.removeAction(action)
+        return menu
+
+    def closeEvent(self, event: QtGui.QCloseEvent) -> None:
+        from PyQt5.QtCore import QEvent
+        if event.type() == QEvent.Close: # on closing the window
+            if self._basefileSave == '':
+                event.accept()
+            else:
+                MessageBox = QtWidgets.QMessageBox(self)
+                MessageBox.setDefaultButton(QtWidgets.QMessageBox.Yes)
+
+                MessageBox.setStandardButtons(QtWidgets.QMessageBox.No | QtWidgets.QMessageBox.Yes|QtWidgets.QMessageBox.Cancel)
+                reply = MessageBox.question(self, 'Close','Do you want to save the changes before closing?',QtWidgets.QMessageBox.No | QtWidgets.QMessageBox.Yes|QtWidgets.QMessageBox.Cancel)
+                if reply == QtWidgets.QMessageBox.Yes:
+                    print('saving the changes ...')
+                    self.saveChanges()
+                    event.accept()
+                elif reply == QtWidgets.QMessageBox.No:
+                    event.accept()
+                elif reply == QtWidgets.QMessageBox.Cancel:
+                    event.ignore()
+
+    #def mousePressEvent(self, a0: QtGui.QMouseEvent) -> None:
+
+            #self.saveChanges()
+
+
+
+
+
+
+def main():
+    app = QtWidgets.QApplication(sys.argv)
+    """
+    
+    # Set the default surface format for the application
+    fmt = QtGui.QSurfaceFormat()
+    fmt.setVersion(2, 0)  # Set the desired OpenGL version
+    fmt.setProfile(QtGui.QSurfaceFormat.CoreProfile)  # Set the desired profile
+    QtGui.QSurfaceFormat.setDefaultFormat(fmt)
+    """
+    root = os.path.dirname(os.path.abspath(__file__))
+    QtCore.QDir.addSearchPath('resource', os.path.join(root, 'resource'))
+    QtCore.QDir.addSearchPath('theme', os.path.join(root, 'resource/theme'))
+    QtCore.QDir.addSearchPath('rc', os.path.join(root, 'resource/theme/rc'))
+    QtCore.QDir.addSearchPath('color', os.path.join(root, 'resource/color'))
+    file = QtCore.QFile("theme:style.qss")
+    file.open(QtCore.QFile.ReadOnly | QtCore.QFile.Text)
+    stream = QtCore.QTextStream(file)
+    app.setStyle(QtWidgets.QStyleFactory.create("Fusion"))
+
+
+    app.setStyleSheet(stream.readAll())
+    window = MainWindow(app=app)
+    window.show()
+    #sys.excepthook = excepthook
+    ret = app.exec_()
+    #print("Exit")
+    #sys.exit(ret)
+    #sys.exc_info()
+
+
+
+
+
+
+
+if __name__ == "__main__":
+    main()
+

melage/requirements22.txt

@@ -0,0 +1,25 @@
+matplotlib==3.4.3 
+nibabel==4.0.2
+numba==0.56.4
+numpy==1.23.5
+opencv_python_headless==4.5.5.64
+pickle5==0.0.11
+pickle-mixin==1.0.2
+Pillow==8.1.1 #strict
+pydicom==2.3.1
+pyFFTW==0.13.0
+PyOpenGL==3.1.6
+PyQt5==5.15.2
+qtwidgets==0.18
+scikit-image==0.19.3
+scikit-learn==1.1.2
+scipy==1.9.2
+SimpleITK==2.2.0
+vtk==9.2.2
+dominate==2.8.0
+rdp==0.8
+Shapely==1.8.4
+cryptography==38.0.2
+trimesh==3.17.0
+torch==1.12.1
+einops==0.6.1

melage/requirements_old.txt

@@ -0,0 +1,28 @@
+scikit-image==0.15.0
+matplotlib==3.3.3
+nibabel==3.2.2
+numba==0.50.1
+opencv_python_headless==4.6.0.66
+pickle-mixin==1.0.2
+Pickle5
+Pillow==8.4.0
+pydicom==2.3.1
+pyFFTW==0.12.00
+PyOpenGL==3.1.6
+PyQt5==5.12.1
+PyQt5_sip==4.19.19
+qtwidgets==0.18
+scikit-learn==0.24.2
+scipy==1.5.4
+SimpleITK==2.1.1
+vtk==9.2.2
+dataclasses==0.6
+Shapely==1.7.1
+dominate==2.6.0
+rdp==0.8
+numpy>=1.19.5
+cryptography==38.0.2
+trimesh==3.17.0
+setuptools>=58.1.0
+torch==1.12.1
+eniops==0.6.1

melage/resource/Eraser_icon.svg

@@ -0,0 +1,79 @@
+<?xml version="1.0" encoding="UTF-8" standalone="no"?>
+<svg
+   xmlns:dc="http://purl.org/dc/elements/1.1/"
+   xmlns:cc="http://creativecommons.org/ns#"
+   xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"
+   xmlns:svg="http://www.w3.org/2000/svg"
+   xmlns="http://www.w3.org/2000/svg"
+   xmlns:sodipodi="http://sodipodi.sourceforge.net/DTD/sodipodi-0.dtd"
+   xmlns:inkscape="http://www.inkscape.org/namespaces/inkscape"
+   version="1.1"
+   width="206.611"
+   height="206.611"
+   viewBox="638.932 206.758 226.611 216.611"
+   id="svg22"
+   sodipodi:docname="Eraser_icon.svg"
+   inkscape:version="0.92.3 (2405546, 2018-03-11)">
+  <metadata
+     id="metadata28">
+    <rdf:RDF>
+      <cc:Work
+         rdf:about="">
+        <dc:format>image/svg+xml</dc:format>
+        <dc:type
+           rdf:resource="http://purl.org/dc/dcmitype/StillImage" />
+      </cc:Work>
+    </rdf:RDF>
+  </metadata>
+  <defs
+     id="defs26" />
+  <sodipodi:namedview
+     pagecolor="#ffffff"
+     bordercolor="#666666"
+     borderopacity="1"
+     objecttolerance="10"
+     gridtolerance="10"
+     guidetolerance="10"
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+     inkscape:pageshadow="2"
+     inkscape:window-width="1853"
+     inkscape:window-height="1025"
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+     showgrid="false"
+     inkscape:lockguides="false"
+     inkscape:zoom="3.2307516"
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