Merge pull request #185 from FanwangM/scale_trans_doc

Add information about accessing translation and scaling

doc/notebooks/Quick_Start.ipynb

@@ -155,6 +155,80 @@
     "print(\"Matrix B (after translation and scaling) = \")\n",
     "print(result.new_b)"
    ]
+  },
+  {
+   "cell_type": "markdown",
+   "id": "6163449e",
+   "metadata": {},
+   "source": [
+    "### Accessing Scaling, Translation Related Information"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "id": "171e4d70",
+   "metadata": {},
+   "source": [
+    "In order to access the scaling factor of the initial two input matrices, we can use `_scale_array` function in `utils` module."
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 2,
+   "id": "09d4f828",
+   "metadata": {},
+   "outputs": [
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "The scaling factor is 0.8623410931853571.\n"
+     ]
+    }
+   ],
+   "source": [
+    "# accessing the scaling factor when preparing two input matrices\n",
+    "from procrustes.utils import _scale_array\n",
+    "\n",
+    "# array_a is scaled to match array_b's norm and the norm of $a$ will be equal norm of $b$\n",
+    "scaled_a, scaling_factor = _scale_array(a, b)\n",
+    "# print(f\"The scaled matrix $a$ is {scaled_a}.\")\n",
+    "print(f\"The scaling factor is {scaling_factor}.\")"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "id": "fc78f6d5",
+   "metadata": {},
+   "source": [
+    "The user may also want to get the translation matrix or the translated matrix. This can be achieved by using `_translate_array` function in `utils` module."
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 3,
+   "id": "0efc68a5",
+   "metadata": {},
+   "outputs": [
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "The centroid is [-0.36907112 -1.20438156 -0.25281312 -0.3612893  -1.00236417 -0.150441\n",
+      " -0.93179808].\n"
+     ]
+    }
+   ],
+   "source": [
+    "# accessing the translation matrix\n",
+    "from procrustes.utils import _translate_array\n",
+    "\n",
+    "# rray_a is translated to centroid of array_b\n",
+    "# the centroid of translated $a$ will centroid with the centroid $b$\n",
+    "trans_array_a, centroid = _translate_array(a, b)\n",
+    "# print(f\"The translated array $a$ is {trans_array_a}.\")\n",
+    "print(f\"The centroid is {centroid}.\")"
+   ]
   }
  ],
  "metadata": {

requirements.txt

@@ -1,4 +1,4 @@
-numpy>=1.21.5
+numpy>=1.19.5
 scipy>=1.5.0
 pytest>=5.4.3
 sphinx>=2.3.0

setup.py

@@ -70,5 +70,5 @@ def get_readme():
         'Topic :: Scientific/Engineering :: Chemistry',
         'Intended Audience :: Science/Research',
     ],
-    install_requires=["numpy>=1.18.5", "scipy>=1.5.0", "pytest>=5.4.3", "sphinx>=2.3.0"],
+    install_requires=["numpy>=1.19.5", "scipy>=1.5.0", "pytest>=5.4.3", "sphinx>=2.3.0"],
 )

tox.ini

@@ -11,12 +11,9 @@ envlist = py36, py37, py38, py39, py310, rst_linux, rst_mac, readme, rst, linter
 
 [testenv]
 deps =
-    pytest
+    -r{toxinidir}/requirements.txt
     pytest-cov
     coverage>=4.2
-    numpy
-    scipy
-    sphinx
 commands =
     # coverage run --rcfile=tox.ini -m pytest tests
     python -m pip install --upgrade pip
@@ -66,8 +63,7 @@ commands = {[testenv:rst_linux]commands}
 
 [testenv:linters]
 deps =
-    numpy
-    scipy
+    -r{toxinidir}/requirements.txt
     pytest
     flake8==4.0.1
     flake8-docstrings==1.6.0