pyIntersecT 0.0.1__tar.gz

pyintersect-0.0.1/.gitignore

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pyintersect-0.0.1/IntersecT.ipynb

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+   "id": "3512ffb9",
+   "metadata": {},
+   "source": [
+    "![IntersecT logo](src/IntersecT/Logo-IntersecT.png)\n",
+    "\n",
+    "\n",
+    "# **IntersecT** \n",
+    "# Qcmp from Perple_X models\n",
+    "---\n",
+    "\n",
+    "## Introduction\n",
+    "Phase diagrams calculated using forward thermodynamic modelling allow users to determine the pressure (*P*) and temperature (*T*) conditions of mineral assemblage formation for a given bulk composition (*X*). In the last decade, several software solutions have provided quantitative approaches where optimal *P–T* conditions can be calculated from a statistical point of view, resulting in a more accurate interpretation of forward model results (e.g., the quality factor implemented in Bingo-Antidote; Duesterhoeft & Lanari, 2020, https://doi.org/10.1111/jmg.12538).\n",
+    "\n",
+    "Here the quality factor of the composition (hereby **Qcmp**) as described in Duesterhoeft & Lanari (2020) is applied to the Perple_X results, particularly from the WERAMI output. The Qcmp allows the propagation of uncertainties in the measured mineral composition. In addition, IntersecT applies a reduced chi-squared statistics to assess the weight of the considered phases. This allows for the down-weighting of outlier data, whether due to model problems or incorrect assumptions, including disequilibrium features.\n",
+    "\n",
+    "##### **Requirements**\n",
+    "- python\n",
+    "- matplotlib\n",
+    "- pandas\n",
+    "- tkinter\n",
+    "- **IntersecT**\n",
+    "\n",
+    "## Install and import the required libraries"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "1c60b3c3-92b4-4fb1-820d-73faab836c59",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "# install the required packages in a local environment\n",
+    "%pip install pyIntersecT"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "de99adbe",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "# import IntersecT\n",
+    "from pyIntersecT import IntersecT\n",
+    "\n",
+    "# create a Quality Factor Analysis object\n",
+    "InT = IntersecT.QualityFactorAnalysis()"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "id": "8d4a90d6",
+   "metadata": {},
+   "source": [
+    "## Input files\n",
+    "Select your **WERAMI output .tab file**, where you extracted the compositions of your phases supposed to be at equilibrium.\n",
+    "\n",
+    "N.B. Because it's required to propagate the uncertainty of the measured composition, the extracted composition should be in **a.p.f.u.**"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "4eceaede",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "# import the output file from Perple_X\n",
+    "InT.import_output_perplex()"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "id": "5f319e23",
+   "metadata": {},
+   "source": [
+    "Select a second **.txt** input file with the **a.p.f.u. measured compositions** that match the WERAMI .tab file, the **name** of the considered phases in your rock and the **color scheme** you wish to apply."
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "dc98d349-0dfb-4b58-a0f6-27237ca9b665",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "# import the measured compositions\n",
+    "InT.import_analytical_compo()"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "id": "3157594d",
+   "metadata": {},
+   "source": [
+    "## Output directory\n",
+    "Select a directory where to store the output."
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "219739c9",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "# set the output directory\n",
+    "InT.set_output_directory()"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "id": "a0b1fc0e",
+   "metadata": {},
+   "source": [
+    "## Qcmp calculation\n",
+    "This part of the code **calculates the Qcmp**\n",
+    "\n",
+    "It then integrates the **reduced chi-squared** statistic to calculate a **weighted Qcmp** based on the best reduced chi-squared value for each phase."
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "id": "69031ecf",
+   "metadata": {},
+   "source": [
+    "This first part calculates the Qcmp for each **element** extracted from the WERAMI output"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "a97a04b1",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "# calculate the quality factor for each element\n",
+    "InT.Qcmp_elem()"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "id": "11e10ec8",
+   "metadata": {},
+   "source": [
+    "This part calculates the Qcmp for each **phase** (combining all elements)"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "23e9f2c6",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "# calculate the quality factor for each phase\n",
+    "Qcmp_phase_tot = InT.Qcmp_phase()"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "id": "85aa1949",
+   "metadata": {},
+   "source": [
+    "This calculates the **reduced chi-squared** for each **phase**"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "74ebb1bd",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "# calculate the reduced chi-squared statistic for each phase\n",
+    "redchi2_phase = InT.redchi2_phase()"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "id": "f28fb481",
+   "metadata": {},
+   "source": [
+    "This calculates the **reduced chi-squared** for the **overall dataset**"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "19aad46a",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "# calculate the reduced chi-squared statistic for the overall dataset\n",
+    "redchi2_allphases = InT.redchi2_tot()"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "id": "dd91529c",
+   "metadata": {},
+   "source": [
+    "This part calculates an **unweighted** Qcmp for the **overall dataset** (combining all phases)"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "996671bc",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "# calculate the unweighted quality factor for the overall dataset\n",
+    "Qcmp_allphases = InT.Qcmp_tot(Qcmp_phase_tot, redchi2_phase)"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "id": "4e783a79",
+   "metadata": {},
+   "source": [
+    "Integrating the reduced chi-squared statistic, this calculates a **weighted Qcmp** for the **overall dataset**"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "5197cdff",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "# calculate the weighted quality factor for the overall dataset\n",
+    "Qcmp_allphases_weight = InT.Qcmp_tot_weight(Qcmp_phase_tot, redchi2_phase)"
+   ]
+  }
+ ],
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