scipy 17 fail

scipy-17.ipynb

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     "text": [
      "0.17.1\n",
      "Dataset is already in place. If you want to fetch it again please first remove the folder /home/shahnawaz/.dipy/ivim \n"
     ]
    },
    {
     "ename": "ValueError",
     "evalue": "`x0` is infeasible.",
     "output_type": "error",
     "traceback": [
      "\u001b[1;31m---------------------------------------------------------------------------\u001b[0m",
      "\u001b[1;31mValueError\u001b[0m                                Traceback (most recent call last)",
      "\u001b[1;32m<ipython-input-3-e49b25282f7f>\u001b[0m in \u001b[0;36m<module>\u001b[1;34m()\u001b[0m\n\u001b[0;32m     20\u001b[0m ivimmodel1 = IvimModel(gtab, x0= np.array([1000., 0.1, 0.001, 0.0001]), bounds=([0., 0., 0., 0.],\n\u001b[0;32m     21\u001b[0m                                                                                [np.inf, 1., 1., 1.]))\n\u001b[1;32m---> 22\u001b[1;33m \u001b[0mivifit\u001b[0m \u001b[1;33m=\u001b[0m \u001b[0mivimmodel1\u001b[0m\u001b[1;33m.\u001b[0m\u001b[0mfit\u001b[0m\u001b[1;33m(\u001b[0m\u001b[0mflat_data\u001b[0m\u001b[1;33m[\u001b[0m\u001b[1;36m8\u001b[0m\u001b[1;33m]\u001b[0m\u001b[1;33m)\u001b[0m\u001b[1;33m\u001b[0m\u001b[0m\n\u001b[0m",
      "\u001b[1;32m/home/shahnawaz/dev/gsoc16/dipy/dipy/reconst/ivim.py\u001b[0m in \u001b[0;36mfit\u001b[1;34m(self, data, mask)\u001b[0m\n\u001b[0;32m    198\u001b[0m                                    \u001b[0mself\u001b[0m\u001b[1;33m.\u001b[0m\u001b[0msplit_b\u001b[0m\u001b[1;33m,\u001b[0m\u001b[1;33m\u001b[0m\u001b[0m\n\u001b[0;32m    199\u001b[0m                                    \u001b[0mself\u001b[0m\u001b[1;33m.\u001b[0m\u001b[0mbounds\u001b[0m\u001b[1;33m,\u001b[0m \u001b[0mself\u001b[0m\u001b[1;33m.\u001b[0m\u001b[0mtol\u001b[0m\u001b[1;33m,\u001b[0m\u001b[1;33m\u001b[0m\u001b[0m\n\u001b[1;32m--> 200\u001b[1;33m                                    self.options)\n\u001b[0m\u001b[0;32m    201\u001b[0m \u001b[1;33m\u001b[0m\u001b[0m\n\u001b[0;32m    202\u001b[0m         \u001b[1;32mif\u001b[0m \u001b[0mmask\u001b[0m \u001b[1;32mis\u001b[0m \u001b[1;32mNone\u001b[0m\u001b[1;33m:\u001b[0m\u001b[1;33m\u001b[0m\u001b[0m\n",
      "\u001b[1;32m/home/shahnawaz/dev/gsoc16/dipy/dipy/reconst/ivim.py\u001b[0m in \u001b[0;36mtwo_stage\u001b[1;34m(data, gtab, x0, split_b, bounds, tol, options)\u001b[0m\n\u001b[0;32m    396\u001b[0m \u001b[1;33m\u001b[0m\u001b[0m\n\u001b[0;32m    397\u001b[0m     _leastsq(flat_data, bvals, flat_x0,\n\u001b[1;32m--> 398\u001b[1;33m              ivim_params, options, tol, bounds)\n\u001b[0m\u001b[0;32m    399\u001b[0m     \u001b[0mivim_params\u001b[0m\u001b[1;33m.\u001b[0m\u001b[0mshape\u001b[0m \u001b[1;33m=\u001b[0m \u001b[0mdata\u001b[0m\u001b[1;33m.\u001b[0m\u001b[0mshape\u001b[0m\u001b[1;33m[\u001b[0m\u001b[1;33m:\u001b[0m\u001b[1;33m-\u001b[0m\u001b[1;36m1\u001b[0m\u001b[1;33m]\u001b[0m \u001b[1;33m+\u001b[0m \u001b[1;33m(\u001b[0m\u001b[1;36m4\u001b[0m\u001b[1;33m,\u001b[0m\u001b[1;33m)\u001b[0m\u001b[1;33m\u001b[0m\u001b[0m\n\u001b[0;32m    400\u001b[0m     \u001b[0mivim_params\u001b[0m\u001b[1;33m[\u001b[0m\u001b[1;33m:\u001b[0m\u001b[1;33m,\u001b[0m \u001b[1;36m0\u001b[0m\u001b[1;33m]\u001b[0m \u001b[1;33m=\u001b[0m \u001b[0mivim_params\u001b[0m\u001b[1;33m[\u001b[0m\u001b[1;33m:\u001b[0m\u001b[1;33m,\u001b[0m \u001b[1;36m0\u001b[0m\u001b[1;33m]\u001b[0m \u001b[1;33m*\u001b[0m \u001b[0mS_normalization\u001b[0m\u001b[1;33m\u001b[0m\u001b[0m\n",
      "\u001b[1;32m/home/shahnawaz/dev/gsoc16/dipy/dipy/reconst/ivim.py\u001b[0m in \u001b[0;36m_leastsq\u001b[1;34m(flat_data, bvals, flat_x0, ivim_params, options, tol, bounds)\u001b[0m\n\u001b[0;32m    321\u001b[0m                                 \u001b[0mgtol\u001b[0m\u001b[1;33m=\u001b[0m\u001b[0mgtol\u001b[0m\u001b[1;33m,\u001b[0m\u001b[1;33m\u001b[0m\u001b[0m\n\u001b[0;32m    322\u001b[0m                                 \u001b[0mmax_nfev\u001b[0m\u001b[1;33m=\u001b[0m\u001b[0mmaxfev\u001b[0m\u001b[1;33m,\u001b[0m\u001b[1;33m\u001b[0m\u001b[0m\n\u001b[1;32m--> 323\u001b[1;33m                                 args=(bvals, flat_data[vox]))\n\u001b[0m\u001b[0;32m    324\u001b[0m             \u001b[0mivim_params\u001b[0m\u001b[1;33m[\u001b[0m\u001b[0mvox\u001b[0m\u001b[1;33m,\u001b[0m \u001b[1;33m:\u001b[0m\u001b[1;36m4\u001b[0m\u001b[1;33m]\u001b[0m \u001b[1;33m=\u001b[0m \u001b[0mres\u001b[0m\u001b[1;33m.\u001b[0m\u001b[0mx\u001b[0m\u001b[1;33m\u001b[0m\u001b[0m\n\u001b[0;32m    325\u001b[0m             \u001b[0mresult\u001b[0m\u001b[1;33m[\u001b[0m\u001b[0mvox\u001b[0m\u001b[1;33m]\u001b[0m \u001b[1;33m=\u001b[0m \u001b[0mres\u001b[0m\u001b[1;33m\u001b[0m\u001b[0m\n",
      "\u001b[1;32m/usr/local/lib/python3.4/dist-packages/scipy/optimize/_lsq/least_squares.py\u001b[0m in \u001b[0;36mleast_squares\u001b[1;34m(fun, x0, jac, bounds, method, ftol, xtol, gtol, x_scale, loss, f_scale, diff_step, tr_solver, tr_options, jac_sparsity, max_nfev, verbose, args, kwargs)\u001b[0m\n\u001b[0;32m    755\u001b[0m \u001b[1;33m\u001b[0m\u001b[0m\n\u001b[0;32m    756\u001b[0m     \u001b[1;32mif\u001b[0m \u001b[1;32mnot\u001b[0m \u001b[0min_bounds\u001b[0m\u001b[1;33m(\u001b[0m\u001b[0mx0\u001b[0m\u001b[1;33m,\u001b[0m \u001b[0mlb\u001b[0m\u001b[1;33m,\u001b[0m \u001b[0mub\u001b[0m\u001b[1;33m)\u001b[0m\u001b[1;33m:\u001b[0m\u001b[1;33m\u001b[0m\u001b[0m\n\u001b[1;32m--> 757\u001b[1;33m         \u001b[1;32mraise\u001b[0m \u001b[0mValueError\u001b[0m\u001b[1;33m(\u001b[0m\u001b[1;34m\"`x0` is infeasible.\"\u001b[0m\u001b[1;33m)\u001b[0m\u001b[1;33m\u001b[0m\u001b[0m\n\u001b[0m\u001b[0;32m    758\u001b[0m \u001b[1;33m\u001b[0m\u001b[0m\n\u001b[0;32m    759\u001b[0m     \u001b[0mx_scale\u001b[0m \u001b[1;33m=\u001b[0m \u001b[0mcheck_x_scale\u001b[0m\u001b[1;33m(\u001b[0m\u001b[0mx_scale\u001b[0m\u001b[1;33m,\u001b[0m \u001b[0mx0\u001b[0m\u001b[1;33m)\u001b[0m\u001b[1;33m\u001b[0m\u001b[0m\n",
      "\u001b[1;31mValueError\u001b[0m: `x0` is infeasible."
     ]
    }
   ],
   "source": [
    "from dipy.reconst.ivim import IvimModel\n",
    "from dipy.data.fetcher import read_ivim\n",
    "import matplotlib.pyplot as plt\n",
    "import numpy as np\n",
    "import scipy\n",
    "\n",
    "print (scipy.__version__)\n",
    "\n",
    "img, gtab = read_ivim()\n",
    "data = img.get_data()\n",
    "\n",
    "x1, x2 = 160, 180\n",
    "y1, y2 = 90, 110\n",
    "z = 33\n",
    "data_slice = data[x1:x2, y1:y2, z, :]\n",
    "\n",
    "flat_data = data_slice.reshape((-1, data.shape[-1]))\n",
    "plt.scatter(gtab.bvals, flat_data[8])\n",
    "\n",
    "ivimmodel1 = IvimModel(gtab, x0= np.array([1000., 0.1, 0.001, 0.0001]), bounds=([0., 0., 0., 0.],\n",
    "                                                                               [np.inf, 1., 1., 1.]))\n",
    "ivifit = ivimmodel1.fit(flat_data[8])"
   ]
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