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Python extension causing an error with numpy

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Join Date: Oct 2007
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Python extension causing an error with numpy

 
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  #1
Feb 11th, 2008
Hello, I have written some python extensions and it seems to be causing a TypeError with numpy.

Here is my code:

python Syntax (Toggle Plain Text) 
  1. import Image, os, sys, gc, numpy, math
  2. sys.path.append("/home/halon/pyxtn")
  3.  
  4. import spam2
  5.  
  6.  
  7. def LoadImages(start, y_stop):
  8.     """Open .tif images, append data to list."""
  9.     global image_data_list, number_of_channels
  10.  
  11.     for i in range(0, number_of_channels):
  12.  
  13.         if i > 0:
  14.             _file= start
  15.             new_channel= '_ch0'+str(i)
  16.             index= _file.index('_ch')
  17.             old_channel= _file[index:index+5]
  18.             _file= _file.replace(old_channel,new_channel)
  19.  
  20.         else:
  21.             _file= start
  22.  
  23.         image= Image.open(_file)
  24.         image_data_list[i].append(list(image.getdata()))
  25.  
  26.         _file, next_slice= YIncrement(y_stop, _file)
  27.  
  28.         while True:
  29.             if next_slice== y_stop:
  30.                 image= Image.open(_file)
  31.                 image_data_list[i].append(list(image.getdata()))
  32.                 break
  33.             else:
  34.                 image= Image.open(_file)
  35.                 image_data_list[i].append(list(image.getdata()))
  36.                 _file, next_slice= YIncrement(y_stop, _file)
  37.  
  38.  
  39.  
  40. def YIncrement(y_stop, file_name):
  41.     """Incement to the next y slice"""
  42.  
  43.     index= file_name.index('_y')
  44.     old= file_name[index:index+5]
  45.     number= old[2:5]
  46.  
  47.     if number[0]== "0" and number[1]== "0":
  48.         number= int(number[2])
  49.     elif number[0]== "0" and number[1]!= "0":
  50.         number= int(number[1]+number[2])
  51.     else:
  52.         number= int(number)
  53.  
  54.     number= str(number+1)
  55.  
  56.     if len(number)== 1:
  57.         y_slice= "_y00"+ number
  58.  
  59.     elif len(number)== 2:
  60.         y_slice= "_y0"+ number
  61.  
  62.     else:
  63.         y_slice= "_y"+ number
  64.  
  65.     _file= file_name.replace(old,y_slice)
  66.  
  67.     return _file, y_slice
  68.  
  69.  
  70. directory= "/home/halon/4pi2"
  71. os.chdir(directory)
  72.  
  73. #Image dimensions
  74. max_x= 512
  75. max_z= 450
  76. max_y= 341
  77. number_of_channels= 1
  78.  
  79. #Name of first and last files in image stack
  80. start= "2007_10_04_SYCP3_MLH1_Stack01_deconv_both_y000_ch00.tif"
  81. stop= "2007_10_04_SYCP3_MLH1_Stack01_deconv_both_y050_ch00.tif"
  82.  
  83. index= stop.index('_y')
  84. y_stop= stop[index:index+5]
  85.  
  86. image_data_list= [[]]
  87.  
  88. LoadImages(start, y_stop)
  89. print "Images loaded..."
  90.  
  91. print "Smothing data..."
  92. for i in range(0, len(image_data_list[0])):
  93.  
  94.     image_data= image_data_list[0][i]
  95.  
  96.     smoothed_data= spam2.Blur_2D(image_data)
  97.     smoothed_data= spam2.Blur_2D(smoothed_data)
  98.     smoothed_data= spam2.Blur_2D(smoothed_data)
  99.  
  100.     image_data_list[0][i]= smoothed_data
  101.  
  102. i= 0 
  103. for image_data in image_data_list[0]:
  104.     max_val= max(image_data)
  105.     limit= spam2.Limit(image_data, 1000, max_val)
  106.     mask= spam2.Threshold(image_data,18)
  107.  
  108.     image_array= numpy.zeros((max_z,max_x,3),numpy.uint8)
  109.  
  110.  
  111.     for x in range(0, max_x):
  112.         for z in range(0, max_z):
  113.             if mask[x+ z*max_x]== 1:
  114.                 image_array[x,z]= [255,255,255]
  115.  
  116.  
  117.     filename= "image"+str(i)+".png"
  118.     image= Image.fromarray(image_array,"RGB")
  119.     image.save(filename)
  120.     i= i+1

When I run this code, the function call on line 105 produces the following error:

Traceback (most recent call last):
File "<stdin>", line 1, in <module>
File "big.py", line 108, in <module>
TypeError: an integer is required

If I comment out line 105, everything is fine. Here is the C code for the function Limit:
C Syntax (Toggle Plain Text) 
  1. //Called from Python as Limit//
  2. static PyObject
  3. *Average(PyObject *self, PyObject *args){
  4.  
  5.   PyObject *input_list, *mask_size, *list_max;
  6.  
  7.   int i, input_list_size, counter, *histogram;
  8.   long sum= 0, max_val, pix_val, pix_in_mask;
  9.   float threshold;
  10.  
  11.   if(!PyArg_ParseTuple(args, "OOO", &input_list, &mask_size, &list_max))
  12.     return NULL;
  13.  
  14.   input_list_size= PyList_Size(input_list);
  15.   pix_in_mask= PyInt_AsLong(mask_size);
  16.   max_val= PyInt_AsLong(list_max);
  17.  
  18.   histogram= malloc(256*sizeof(int));
  19.  
  20.   for(i= 0; i<= 255; i++) histogram[i]= 0;
  21.  
  22.   for(i= 0; i<= input_list_size; i++){
  23.     pix_val= PyInt_AsLong(PyList_GetItem(input_list,i));
  24.  
  25.     if(pix_val >0)
  26.         histogram[pix_val]++;
  27.   }
  28.  
  29.   counter= 0;
  30.   i= 255;
  31.  
  32.   do{
  33.     counter += histogram[i];
  34.     i--;
  35.  
  36.   } while((counter < pix_in_mask)&&(i>0));
  37.  
  38.   threshold= (float)i /255.;
  39.  
  40.   return Py_BuildValue("f", threshold);
  41.  
  42. }

Any help is appreciated!!!!! Thanks.
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