Updated requirements

README.md

@@ -1,6 +1,19 @@
 # GradientDesignTool
+
+
 A design tool for creating gradient coils for Halbach array based MRI systems based on the Target Field Method initially proposed by Turner.
 
 Run gradientDesignTool.py to load the GUI. 
 
+```bash
+$ git clone --depth 1 https://github.com/LUMC-LowFieldMRI/GradientDesignTool GradientDesignTool
+$ cd GradientDesignTool
+$ python -m venv venv
+$ source venv/bin/activate
+$ pip install -r requirements.txt
+$ python ./gradientDesignTool.py
+```
+
 Note; The tool is fully functional but still in an early beta version and can be unstable. A known issue is that the outer-most wires can be open, this will cause problems in simulating the gradient fields and will cause the wire export to be stuck in a permanent loop. Tweaking the parameters can eliminate the open wires (setting the number of higher order modes to 0 seems to work well).
+
+![gradientDesignTool screenshot](./documentation/images/gradientDesignTool.png)

documentation/images/.gitignore

@@ -0,0 +1 @@
+

gradientCalculationV2_1.py

@@ -51,7 +51,7 @@ def halbachXgradient(linearLength = 140, coilRad = 135, coilLength = 350,numWire
     N               = numHighOrders
     h               = apoTerm
 
-    Nsamp           = np.int(2*Zmax/res)
+    Nsamp           = int(2*Zmax/res)
     z               = np.linspace(-Zmax,Zmax,Nsamp)
     phi             = np.linspace(-1.5*np.pi,0.5*np.pi,Nsamp)
 
@@ -91,7 +91,7 @@ def halbachYgradient(linearLength = 140, coilRad = 135, coilLength = 350, numWir
     print("Number of higher order modes set to 0, not needed for Y and Z")
     h               = apoTerm
 
-    Nsamp           = np.int(2*Zmax/resolution)
+    Nsamp           = int(2*Zmax/resolution)
     z               = np.linspace(-Zmax,Zmax,Nsamp)
     phi             = np.linspace(-np.pi,np.pi,Nsamp)
 
@@ -134,7 +134,7 @@ def halbachZgradient(linearLength = 140, coilRad = 135, coilLength = 350, numWir
     #print("Number of higher order modes set to 0, not needed for Y and Z")
     h               = apoTerm
 
-    Nsamp           = np.int(2*Zmax/resolution)
+    Nsamp           = int(2*Zmax/resolution)
     z               = np.linspace(-Zmax,Zmax,Nsamp)
     phi             = np.linspace(-np.pi,np.pi,Nsamp)+np.pi/4
 
@@ -193,7 +193,7 @@ def calculateBfield(contours, DSV, resolution, coilRad, direction):
     wireCounter = 1
     for wireLevel in wireLevels:
         for wire in wireLevel:
-            print("Simulating wire %.0f of %0.f"%(wireCounter, np.size(wireLevels)))
+            #print("Simulating wire %.0f of %0.f"%(wireCounter, wireLevels))
             wire = np.array(wire, dtype = np.float32)
             wirePath3D =  np.stack((np.cos(wire[:,0])*np.float32(coilRad),np.sin(wire[:,0])*np.float32(coilRad),wire[:,1]),axis=1)
             idS = 1e-7*gradCurrent*(wirePath3D[1:,:] - wirePath3D[:-1,:])
@@ -296,54 +296,3 @@ def exportWires(contours, coilRad, direction, conjoined):
             joinedContour[key] = np.delete(joinedContour[key],np.nonzero(zeroElements), axis = 0)
 
         return joinedContour
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gradientDesignTool.py

@@ -218,7 +218,7 @@ def calculateGradientWires(self):
         self.contourfig.gca().set_xlabel('Z (mm)')
         self.contourfig.gca().set_ylabel('Y (mm)')
         self.contourfig.gca().set_zlabel('X (mm)')
-        np.warnings.filterwarnings('ignore', category=np.VisibleDeprecationWarning)                 
+        #np.warnings.filterwarnings('ignore', category=np.VisibleDeprecationWarning)                 
         self.length = 0
         for idx, wireLevel in enumerate(wireLevels):
             currentLevel = self.contourData.levels[idx]
@@ -306,4 +306,4 @@ def exportWireCSV(self):
 
 app = GDT_GUI()
 app.mainloop()
-closePlots('all')
+closePlots('all')

requirements.txt

@@ -1,8 +1,11 @@
-cycler==0.10.0
-kiwisolver==1.2.0
-matplotlib==3.2.1
-numpy==1.18.3
-pyparsing==2.4.7
-python-dateutil==2.8.1
-scipy==1.4.1
-six==1.14.0
+cycler==0.12.1
+Cython==3.0.10
+kiwisolver==1.4.5
+matplotlib==3.2.0rc1
+numexpr==2.10.0
+numpy==1.26.4
+pybind11==2.12.0
+pyparsing==3.1.2
+python-dateutil==2.9.0.post0
+scipy==1.13.1
+six==1.16.0