Unit tests, small API changes and updated notebooks

Author: tritemio

notebooks/PyBroMo - 1. Simulate 3D trajectories - single core.ipynb

@@ -79,6 +79,12 @@
     "rs = np.random.RandomState(seed=1)\n",
     "print('Initial random state:', pbm.hash_(rs.get_state()))\n",
     "\n",
+    "# Simulation time step (seconds)\n",
+    "t_step = 0.5e-6\n",
+    "\n",
+    "# Time duration of the simulation (seconds)\n",
+    "t_max = 1\n",
+    "\n",
     "# Diffusion coefficient\n",
     "Du = 12.0            # um^2 / s\n",
     "D1 = Du*(1e-6)**2    # m^2 / s\n",
@@ -87,18 +93,14 @@
     "# Simulation box definition\n",
     "box = pbm.Box(x1=-4.e-6, x2=4.e-6, y1=-4.e-6, y2=4.e-6, z1=-6e-6, z2=6e-6)\n",
     "\n",
-    "# PSF definition\n",
-    "psf = pbm.NumericPSF()\n",
-    "\n",
     "# Particles definition\n",
-    "P = pbm.Particles(num_particles=2, D=D1, box=box, rs=rs)\n",
-    "P.add(num_particles=3, D=D2)\n",
-    "\n",
-    "# Simulation time step (seconds)\n",
-    "t_step = 0.5e-6\n",
+    "P = pbm.Particles.from_specs(\n",
+    "    num_particles=(3, 1),\n",
+    "    D=(D1, D2),\n",
+    "    box=box, rs=rs)\n",
     "\n",
-    "# Time duration of the simulation (seconds)\n",
-    "t_max = 1\n",
+    "# PSF definition\n",
+    "psf = pbm.NumericPSF()\n",
     "\n",
     "# Particle simulation definition\n",
     "S = pbm.ParticlesSimulation(t_step=t_step, t_max=t_max, \n",
@@ -215,16 +217,6 @@
     "print('Current random state:', pbm.hash_(rs.get_state()))"
    ]
   },
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "metadata": {},
-   "outputs": [],
-   "source": [
-    "position = S.position[:]\n",
-    "position.shape, position.dtype"
-   ]
-  },
   {
    "cell_type": "markdown",
    "metadata": {},
@@ -252,19 +244,19 @@
    ]
   },
   {
-   "cell_type": "code",
-   "execution_count": null,
+   "cell_type": "markdown",
    "metadata": {},
-   "outputs": [],
    "source": [
-    "S.compact_name()"
+    "# Load trajectories"
    ]
   },
   {
-   "cell_type": "markdown",
+   "cell_type": "code",
+   "execution_count": null,
    "metadata": {},
+   "outputs": [],
    "source": [
-    "# Load trajectories"
+    "S.hash()"
    ]
   },
   {
@@ -273,8 +265,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "#S = pbm.ParticlesSimulation.from_datafile('9125')  # Read-only by default\n",
-    "S = pbm.ParticlesSimulation.from_datafile('4500')"
+    "S = pbm.ParticlesSimulation.from_datafile(S.hash()[:4])  # Read-only by default"
    ]
   },
   {
@@ -413,33 +404,6 @@
     "S.store.close()"
    ]
   },
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "metadata": {},
-   "outputs": [],
-   "source": [
-    "S.ts_store.close()"
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "metadata": {},
-   "outputs": [],
-   "source": [
-    "S.compact_name()"
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "metadata": {},
-   "outputs": [],
-   "source": [
-    "S.position"
-   ]
-  },
   {
    "cell_type": "markdown",
    "metadata": {},
@@ -510,7 +474,7 @@
    "source": [
     "ts_params2 = dict(\n",
     "    max_rates=(250e3, 180e3), \n",
-    "    populations=(slice(0,2), slice(2, 2+3)),\n",
+    "    populations=(slice(0,3), slice(3, 3+1)),\n",
     "    bg_rate=1.2e3\n",
     ")\n",
     "\n",
@@ -658,7 +622,7 @@
     "width": "212px"
    },
    "toc_section_display": "block",
-   "toc_window_display": true
+   "toc_window_display": false
   }
  },
  "nbformat": 4,