IO: adding example for MannBox file

Author: ebranlard

data/example_files/MannBox_32x4x8.bin

@@ -0,0 +1,90 @@
+""" 
+Example usage for the MannBox class.
+"""
+
+import os
+import numpy as np
+import matplotlib.pyplot as plt
+from pyFAST.input_output.mannbox_file import MannBoxFile
+
+
+scriptDir = os.path.dirname(__file__)
+
+# --- Inputs
+file_u = os.path.join(scriptDir, '../../../data/example_files/MannBox_32x4x8.bin')
+dy = 3  # horizontal spacing [m]
+dz = 10 # vertical spacing [m]
+
+# --- Read Mann Box file and display main properties
+mb = MannBoxFile(file_u, dy=dy, dz=dz) # create a MannBoxFile object, store it in mb
+print(mb)                        # print misc info about the object
+print(mb['field'].shape)         # print the shape of your field. 
+nx, ny, nz =  mb['field'].shape  # Store the field dimension
+
+
+# --- Plot values of the field at given indices. Note this example has only 2 values in x
+# NOTE: can also be obtained directly using: 
+# u = mb.valuesAt(y=5, z=50)
+t = mb.t(dx=1, U=10)
+u = mb['field'][:, 3, 5] # Value at indices iy=3, iz=5
+plt.figure(1)
+plt.plot(t, u, label='Input') 
+plt.xlabel('time [s]') 
+plt.ylabel('u [m/s]')
+plt.title('Value of field at chosen location as function of x/t')
+
+
+# --- Plot vertical profile averaged over all x and y
+# NOTE: can also be obtained directly using: 
+#    z, means, stds = mb.vertProfile
+u_mean_vertical = np.mean(np.mean(mb['field'][:,:,:], axis=0), axis=0)
+plt.figure(2)
+plt.plot(u_mean_vertical, mb.z, label='Input') 
+plt.xlabel('u mean [m/s]') 
+plt.ylabel('z [m]')
+plt.title('Average vertical profile for all x and y')
+
+# --- Compute the mean over all "x" values for each points in the y-z plane
+UmeanYZ = np.mean(mb['field'][:,:,:],axis=0) # This has shape ny x nz
+
+# --- Modify the field  (some examples)
+mb['field'] -= UmeanYZ         # remove the mean of all datapoints along x 
+mb['field'][:,:,:] *= 2        # multiply the field by 10 everywhere
+mb['field'][:,:,:] += UmeanYZ  # add the mean again
+mb['field'][:,:,:] += 0.5      # add 0.5 everywhere in the field
+mb['field'][:,:,0] = 0         # set the velocity to be zero for the first z index
+
+
+# --- Plot value of the field again
+u = mb['field'][:, 3, 5] # Value at indices iy=3, iz=5
+plt.figure(1)
+plt.plot(t, u, label='Modified') 
+plt.xlabel('time [s]') 
+plt.ylabel('u [m/s]')
+
+# --- Plot the vertical profile again
+u_mean_vertical2 = np.mean(np.mean(mb['field'][:,:,:], axis=0), axis=0)
+plt.figure(2)
+plt.plot(u_mean_vertical2, mb.z, '--', label='Modified') 
+plt.xlabel('u mean [m/s]') 
+plt.ylabel('z [m]')
+
+
+
+
+# --- Write the modified field to disk with another filename
+outFile = file_u.replace('.bin','_modified.bin')
+mb.write(outFile) 
+print('File written: ', outFile)
+
+
+
+if __name__ == "__main__":
+    plt.show()
+
+if __name__=='__test__':
+    try:
+        os.remove(outFile)
+    except:
+        pass
+

pyFAST/input_output/examples/Example_MannBox.py

@@ -47,8 +47,8 @@ class MannBoxFile(File):
         print(mb['field'].shape)  
 
         # Use methods to extract relevant values
-        u,v,w = my.valuesAt(y=10.5, z=90)
-        z, means, stds = mb.vertProfile()
+        u = mb.valuesAt(y=10.5, z=90)
+        z, means, stds = mb.vertProfile
 
         # Write to a new file
         mb.write('Output_1024x16x16.u')
@@ -119,6 +119,7 @@ def read(self, filename=None, N=None, dy=1, dz=1, y0=None, z0=0, zMid=None):
             else:
                 raise BrokenFormatError('Reading a Mann box requires the knowledge of the dimensions. The dimensions can be inferred from the filename, for instance: `filebase_1024x32x32.u`. Try renaming your file such that the three last digits are the dimensions in x, y and z.')
         nx,ny,nz=N
+
         def _read_buffered():
             data=np.zeros((nx,ny,nz),dtype=np.float32)
             with open(self.filename, mode='rb') as f:            
@@ -143,10 +144,6 @@ def _read_nonbuffered():
         self['y0']=y0
         self['z0']=z0
         self['zMid']=zMid
-#         print('1',self['field'][:,-1,0])
-#         print('2',self['field'][0,-1::-1,0])
-#         print('3',self['field'][0,-1,:])
-
 
     def write(self, filename=None):
         """ Write mann box """
@@ -169,11 +166,13 @@ def __repr__(self):
         s+='|   min: {}, max: {}, mean: {} \n'.format(np.min(self['field']), np.max(self['field']), np.mean(self['field']))
         s+='| - dy, dz:  {}, {}\n'.format(self['dy'], self['dz'])
         s+='| - y0, z0 zMid:  {}, {}, {}\n'.format(self['y0'], self['z0'], self['zMid'])
-        s+='|useful getters: y, z, _iMid, fromTurbSim\n'
         z=self.z
         y=self.y
-        s+='|   y: [{} ... {}],  dy: {}, n: {} \n'.format(y[0],y[-1],self['dy'],len(y))
-        s+='|   z: [{} ... {}],  dz: {}, n: {} \n'.format(z[0],z[-1],self['dz'],len(z))
+        s+='| * y: [{} ... {}],  dy: {}, n: {} \n'.format(y[0],y[-1],self['dy'],len(y))
+        s+='| * z: [{} ... {}],  dz: {}, n: {} \n'.format(z[0],z[-1],self['dz'],len(z))
+        s+='|useful functions:\n'
+        s+='| - t(dx, U)\n'
+        s+='| - valuesAt(y,z), vertProfile, fromTurbSim(*), _iMid()\n'
         return s
 
 

pyFAST/input_output/mannbox_file.py

@@ -0,0 +1 @@
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pyFAST/input_output/tests/example_files/MannBox_2x4x8.bin

@@ -0,0 +1,23 @@
+import unittest
+import os
+import numpy as np
+from pyFAST.input_output.mannbox_file import MannBoxFile
+from pyFAST.input_output.tests.helpers_for_test import MyDir, reading_test 
+
+class Test(unittest.TestCase):
+
+    def test_001_read_all(self, DEBUG=True):
+        reading_test('MannBox_*.*', MannBoxFile)
+
+    def test_MannBox(self):
+        # --- Test read/write
+        F = MannBoxFile(os.path.join(MyDir,'MannBox_2x4x8.bin'))
+        F.write(        os.path.join(MyDir,'MannBox_2x4x8_TMP.bin'))
+        F2= MannBoxFile(os.path.join(MyDir,'MannBox_2x4x8_TMP.bin'))
+        os.remove(      os.path.join(MyDir,'MannBox_2x4x8_TMP.bin'))
+        np.testing.assert_almost_equal(F['field'].shape ,[2,4,8])
+        np.testing.assert_almost_equal(F['field'][:,:,:],F2['field'][:,:,:],8)
+        np.testing.assert_almost_equal(F['field'][1,3,5], -3.6654968, 6) 
+
+if __name__ == '__main__':
+    unittest.main()