pyMinColab02.ipynb

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        "<a href=\"https://colab.research.google.com/github/mzucali/pyMinColab/blob/main/pyMinColab02.ipynb\" target=\"_parent\"><img src=\"https://colab.research.google.com/assets/colab-badge.svg\" alt=\"Open In Colab\"/></a>"
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      "cell_type": "markdown",
      "source": [
        "# pyMIN Colab version\n",
        "January 2023 - first attempt to move pyMin to colab notebook\n",
        "\n",
        "by **Michele Zucali**, Department of Earth Sciences - University of Milan - Italy\n",
        "\n",
        "[https://github.com/mzucali/pyMinColab](https://github.com/mzucali/pyMinColab)"
      ],
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      "source": [
        "This is a **basic code** to re-calculate mineral structural formula for rock-forming mineral starting from SEM-EMPA data, Wt% of oxides (e.g., SiO2, Al2O3, MgO, etc.).\n",
        "\n",
        "\n",
        "---\n",
        "\n",
        "\n",
        "### INPUT FILE PREPARATION\n",
        "1) **INPUT** file format is preferibly XLSX but XLS, TAB, CSV, TXT are also accepted.\n",
        "\n",
        "2) **MANDATORY** **headers** are **Sample, Mineral** and **oxides** names (e.g. SiO2, Al2O3, MgO, etc.). Case **INSENSITIVE**, so SIO2, SIo2, SiO2, sio2, siO2, sIo2, ALL accepted!\n",
        "\n",
        "3) **REMOVE** any column with numerical data NOT oxides names (e.g., TOTAL), but you can leave any text comment\n",
        "\n",
        "4) **SAMPLE** column is FREE and reports sample your labels (e.g., 2mZB26_domain2_Grt34)\n",
        "\n",
        "5) **MINERAL** column is **mandatory** and report a label specific for the mineral phase (e.g., grt, als, ttn, amp, etc...). Mineral has a **specific** list with a large number of cases.\n",
        "\n",
        "HERE links to an **[Example_INPUT_FILE](https://github.com/mzucali/pyMinColab/blob/8f00b4148f715caabdbe38331063c9e9c2679e84/testData/example_input_file.xlsx)** (xlsx) [https://github.com/mzucali/pyMinColab/blob/8f00b4148f715caabdbe38331063c9e9c2679e84/testData/example_input_file.xlsx] and **[MINERAL_lables](https://github.com/mzucali/pyMinColab/blob/8f00b4148f715caabdbe38331063c9e9c2679e84/testData/labelsMIN.xlsx)** [https://github.com/mzucali/pyMinColab/blob/8f00b4148f715caabdbe38331063c9e9c2679e84/testData/labelsMIN.xlsx]"
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    {
      "cell_type": "markdown",
      "source": [
        "**HOW TO RUN your INPUT File**\n",
        "\n",
        "\n",
        "---\n",
        "\n",
        "\n",
        "1) select Run All from Runtime menu\n",
        "\n",
        "2) select Choose Files form the button appeared at the bottom of this page (as your run Run All not before)\n",
        "\n",
        "3) it will start the computation with a LONG list of outputs as it finished a folder **mydata** will be created with your **input** file, the **output** file (inputfilename_OUT)\n",
        "\n",
        "4) you can download the output"
      ],
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    {
      "cell_type": "markdown",
      "source": [
        "Import statements"
      ],
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      "cell_type": "code",
      "execution_count": null,
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      "outputs": [],
      "source": [
        "print(\"GitHub\")\n",
        "!git clone https://www.github.com/mzucali/pyMinColab.git\n",
        "%cd /content/pyMinColab/\n",
        "!pip install pandas_path\n",
        "from mincalclib import dataset"
      ]
    },
    {
      "cell_type": "markdown",
      "source": [
        "***choose your File from the button below***, **XLSX (preferred)** or xls, csv, tab, txt"
      ],
      "metadata": {
        "id": "3XELn2AiI52m"
      }
    },
    {
      "cell_type": "code",
      "source": [
        "!mkdir '/content/pyMinColab/mydata'\n",
        "%cd /content/pyMinColab/mydata/\n",
        "from google.colab import files\n",
        "uploaded = list(files.upload())[0]\n",
        "print(\"uploaded file: \", uploaded)\n",
        "dataset.dataset(uploaded) # RUN pyMin calculation\n",
        "print(\"JOB COMPLETED SUCCESSFULLY\")\n",
        "%cd /content/"
      ],
      "metadata": {
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      "execution_count": null,
      "outputs": []
    },
    {
      "cell_type": "markdown",
      "source": [
        "**DOWNLOAD YOUR FILE from myData before closing.**"
      ],
      "metadata": {
        "id": "8thJ42KVGnVO"
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    },
    {
      "cell_type": "markdown",
      "source": [
        "11th January 2023, it works!\n",
        "by Michele Zucali\n",
        "https://github.com/mzucali/pyMinColab/"
      ],
      "metadata": {
        "id": "3io0zalOem_E"
      }
    },
    {
      "cell_type": "markdown",
      "source": [
        "Updates\n",
        "- November 2023"
      ],
      "metadata": {
        "id": "qpd9CIjmztsC"
      }
    }
  ]
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