py2ls 0.1.0__py3-none-any.whl

py2ls/README.md

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+## ips
+
+### listdir, basename, dirname, newfolder
+
+e.g., 
+
+```python
+fpath = "....../"
+ips.listdir(fpath, kind='pdf', sort_by="size", ascending=0, output = df)
+```
+
+it filters the ‘.pdf’ files, and sort by the (file-size/name, length of name, create_time, mod_time, last_open_time …) it returns a DataFrame or BoxList (setting by ‘output’)
+
+```python
+dir_data, dir_fig = newfolder(fpath, {'data', 'fig'}) # create folder
+```
+
+```python
+finfo(fpath) # get info: size, creation time, mod time, parent_path, fname, kind...
+```
+
+```python
+dir_lib(lib_of_interest) # get the fpath
+```
+
+
+
+### list_func/func_list (same)
+
+list functions in a package
+
+### fload, fsave, figsave
+
+e.g., 
+
+```python
+fload(fpath, kind=None, **kwargs)
+```
+
+load file (docx, pdf, image, md, json,csv,txt, html, yaml, xml, xlsx…) or save file.
+
+```python
+# figsave, as used in matlab. 
+figsave(dir_save, "fname.pdf", dpi=300)
+```
+
+
+
+### pdf2img, img2pdf, docx2pdf
+
+extract images from a PDF, or merge images into a pdf file
+
+```python
+pdf2img(dir_pdf, dir_save=None, page=None, kind="png",verbose=True, **kws)
+pdf2img(fpath, page=[None, None])  # means extract all pages
+# processing page: 1
+# processing page: 2
+# processing page: 3
+# processing page: 4
+# processing page: 5
+
+```
+
+```python
+img2pdf(dir_img, kind="jpeg",page=None, dir_save=None, page_size="a4", dpi=300)
+```
+
+```python
+docx2pdf(dir_docx, dir_save) # convert docx to pdf
+```
+
+### paper_size
+
+quickly get the size info
+
+```python
+paper_size('a4') # [210, 297]
+paper_size('card') # [85.6, 53.98]
+```
+
+
+
+### str2num, num2str, str2list
+
+e.g., 
+
+```python
+str2num(“123.345 dollers”,2)# => 123.35 (float) 
+```
+
+```python
+str2list("abcd") # ['a','b','c','d']
+```
+
+```python
+list2str(x_str)
+```
+
+
+
+### ssplit, sreplace
+
+```python
+sreplace(text, dict_replace=None, robust=True)
+```
+
+```python
+ssplit(text, by="space", verbose=False, **kws) # by = "word", "sentence", ", ","num_strings","digital".....,"length", "upper followed lower", "lower followed upper"
+```
+
+```python
+text = "The most pronounced physiological changes in sleep occur in the brain.[10] The brain uses significantly less energy during sleep than it does when awake, especially during non-REM sleep. In areas with reduced activity, the brain restores its supply of adenosine triphosphate (ATP), the molecule used for short-term storage and transport of energy.[11] In quiet waking, the brain is responsible for 20% of the body's energy use, thus this reduction has a noticeable effect on overall energy consumption.[12]"
+ssplit(text, by=["[10]", "[11]", "[12]"])
+# ['The most pronounced physiological changes in sleep occur in the brain.',
+# ' The brain uses significantly less energy during sleep than it does when awake, especially during non-REM sleep. In areas with reduced activity, the brain restores its supply of adenosine triphosphate (ATP), the molecule used for short-term storage and transport of energy.',
+# " In quiet waking, the brain is responsible for 20% of the body's energy use, thus this reduction has a noticeable effect on overall energy consumption.",
+ # '']
+```
+
+```python
+ssplit(text[:30], by="len", length=5)
+# ['The m', 'ost p', 'ronou', 'nced ', 'physi', 'ologi']
+```
+
+```python
+ssplit(text, by="non_alphanumeric")
+# ['The most pronounced physiological changes in sleep occur in the brain.[',
+#  '10',
+#  '] The brain uses significantly less energy during sleep than it does when awake, especially during non-REM sleep. In areas with reduced activity, the brain restores its supply of adenosine triphosphate (ATP), the molecule used for short-term storage and transport of energy.[',
+#  '11',
+#  '] In quiet waking, the brain is responsible for ',
+#  '20',
+#  "% of the body's energy use, thus this reduction has a noticeable effect on overall energy consumption.[",
+#  '12',
+#  ']']
+```
+
+```python
+ssplit(text, by="sent")
+#['The most pronounced physiological changes in sleep occur in the brain.',
+ #'[10] The brain uses significantly less energy during sleep than it does when awake, especially during non-REM sleep.',
+ #'In areas with reduced activity, the brain restores its supply of adenosine triphosphate (ATP), the molecule used for short-term storage and transport of energy.',
+ #"[11] In quiet waking, the brain is responsible for 20% of the body's energy use, thus this reduction has a noticeable effect on overall energy consumption.",
+ #'[12]']
+```
+
+```python
+ssplit(text, by="lowup")
+# ["The most pronounced physiological changes in sleep occur in the brain.[10] The brain uses significantly less energy during sleep than it does when awake, especially during non-REM sleep. In areas with reduced activity, the brain restores its supply of adenosine triphosphate (ATP), the molecule used for short-term storage and transport of energy.[11] In quiet waking, the brain is responsible for 20% of the body's energy use, thus this reduction has a noticeable effect on overall energy consumption.[12]"]
+
+```
+
+
+
+### stats
+
+#### **FuncCmpt** ( two groups cmp)
+
+```python
+FuncCmpt(X1, X2, pmc='auto', pair='unpaired')
+```
+
+#### FuncMultiCmpt ( multiple groups cmp)
+
+```python
+FuncMultiCmpt(pmc='pmc', pair='unpair', data=None, dv=None, factor=None,
+                  ss_type=2, detailed=True, effsize='np2',
+                  correction='auto', between=None, within=None,
+                  subject=None, group=None
+                  )
+```
+
+
+
+#### FuncStars
+
+```python
+FuncStars(ax,
+              pval=None,
+              Ylim=None,
+              Xlim=None,
+              symbol='*',
+              yscale=0.95,
+              x1=0,
+              x2=1,
+              alpha=0.05,
+              fontsize=14,
+              fontsize_note=6,
+              rotation=0,
+              fontname='Arial',
+              values_below=None,
+              linego=True,
+              linestyle='-',
+              linecolor='k',
+              linewidth=.8,
+              nsshow='off',
+              symbolcolor='k',
+              tailindicator=[0.06, 0.06],
+              report=None,
+              report_scale=-0.1,
+              report_loc=None)
+```
+
+### plots
+
+#### stdshade
+
+```python
+stdshade(ax=None,*args, **kwargs)
+```
+
+#### add_colorbar
+
+```python
+add_colorbar(im, width=None, pad=None, **kwargs)
+```
+
+#### get_color
+
+```python
+get_color(n=1, cmap='auto')
+```
+
+```python
+get_color(12)
+# ['#474747',
+#  '#FF2C00',
+#  '#0C5DA5',
+#  '#845B97',
+#  '#58BBCC',
+#  '#FF9500',
+#  '#D57DBE',
+#  '#474747',
+#  '#FF2C00',
+#  '#0C5DA5',
+#  '#845B97',
+#  '#58BBCC']
+```
+
+
+
+#### img appearance
+
+#### imgsets
+
+```python
+imgsets(
+    img,
+    sets=None,
+    show=True,
+    show_axis=False,
+    size=None,
+    dpi=100,
+    figsize=None,
+    auto=False,
+    filter_kws=None,
+)
+```
+
+```python
+img = imgsets(
+    fpath,
+    sets={"rota": -5, "sharp": 10},
+    dpi=200,
+    # show_axis=True,
+)
+figsave(dir_save, "test1_sharp.pdf")
+
+
+img2 = imgsets(
+    fpath,
+    sets={"rota": -5, "crop": [100, 100, 300, 400], "sharp": 10},
+    dpi=200,
+    filter_kws={
+        "sharpen": 10,
+    },
+    # show_axis=True,
+)
+figsave(dir_save, "test2_crop.pdf")
+```
+
+```python
+fload(dir_img)
+```
+
+![image-20240613233304196](./README.assets/image-20240613233304196.png)
+
+```python
+imgsets(img, sets={"color": 1.5}, show=0)
+```
+
+![image-20240613233356996](./README.assets/image-20240613233356996.png)
+
+```python
+imgsets(img, sets={"pad": (300, 300), "bgcolor": (73, 162, 127)}, show=0)
+```
+
+![image-20240613233423144](./README.assets/image-20240613233423144.png)
+
+```python
+imgsets(
+    img,
+    sets={"contrast": 1.3, "color": 1.5, "pad": (300, 300)},
+    show=0,
+    filter_kws=dict(sh=1050, EDG=10, gaus=5),
+)
+```
+
+![image-20240613233503718](./README.assets/image-20240613233503718.png)
+
+```python
+imgsets(
+    img,
+    sets={"color": 10.5},
+    show=0,
+    filter_kws=dict(EDGE_ENHANCE=50, EDGE_NHANCEmore=50),
+)
+```
+
+![image-20240613233525291](./README.assets/image-20240613233525291.png)
+
+```python
+imgsets(
+    img,
+    sets=dict(contr=1.5, rm="default"),
+    show=0,
+    # filter_kws=dict(sharp=1),
+)
+```
+
+![image-20240613233554225](./README.assets/image-20240613233554225.png)
+
+```python
+imgsets(
+    img,
+    sets=dict(contr=0, rm="default"),
+    show=0,
+    filter_kws=dict(sharp=1),
+)
+```
+
+![image-20240613233611627](./README.assets/image-20240613233611627.png)
+
+#### figsets
+
+```python
+figsets(*args)
+```
+
+```python
+cm = 1 / 2.54
+# plt.style.use("paper")
+plt.figure(figsize=[8 * cm, 5 * cm])
+for i in range(2, 4):
+    plt.plot(x, y * i, ls="-")
+figsets(
+    plt.gca(),
+    {
+        "xlabel": f"time([{x[0]}:{x[-1]}])",
+        "ylabel": "Amplitude (signals)",
+        # "titel": "paper",
+        "xlim": [0, 600],
+        "xtick": np.arange(0, 620, 150),
+        "xlabel": "test xticklabel",
+        # "ylim": [-2.5, 2.5],
+        "sp": "go",
+        # "style": "paper",
+        "box": ":",
+        "grid": "on",
+        "minorticks": "on",
+        "ticks": {"c": "k"},
+    },
+)
+figsets('style','paper')
+```
+
+```python
+cm = 1/2.54  # centimeters in inches
+fig, ax = plt.subplots(1, 1, figsize=(7*cm, 5*cm))
+x = np.linspace(0, 2 * np.pi, 50) * 100
+y = np.sin(x)
+c=get_color(7)
+
+for i in range(2,7):
+    plt.plot(x, y*i,c=c[i])
+figsets(
+    ax,
+    {
+        "xlim": [0, 450],
+        # "ylim": [-1.5, 1.5],
+        "xlabel": "2222",
+        # "style":"paper",
+        "yticks": np.arange(-5,5, 2),
+        "ylabel": "ylabelsssss",
+        "xtkbel": range(0, 800, 100),
+        # "spine": 5,
+        "suptitle": "supertitle",
+        # "minorticks": "y",
+        # "ticksloc":"lt",
+        # "ticks": {"direction": "out",'c':'b'},
+        "rotation":45,
+        # 'box':"lt",
+        # "labellocation":'r',
+        # "ax_color":'b',
+        # 'grid':{"which":'minor','lw':1,"ls":'-.','c':'b','al':0.3},
+    },
+)
+```
+

py2ls/__init__.py

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+"""
+    __init__ of the pyos module
+"""
+
+from . import (
+    brain_atlas, 
+    correlators, 
+    dbhandler, 
+    freqanalysis, 
+    internet_finder, 
+    ips, 
+    netfinder, 
+    sleep_events_detectors, 
+    translator, 
+    version, 
+    wb_detector, 
+    )

py2ls/brain_atlas.py

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+import requests
+from PIL import Image
+from io import BytesIO
+import os
+
+
+def atlas_url(ml, ap, dv, kind="rat"):
+    """
+    Constructs the URL for the rat or mouse brain atlas API based on the provided coordinates.
+    In neuroscience, ML, AP, and DV coordinates are commonly used to specify locations within 
+    the brain. Here's what they stand for:
+
+    Args:
+    ML(float): Medio-lateral coordinate. It refers to the position along the medial-lateral axis of 
+        the brain. The medio-lateral axis runs from the midline (medial) to the sides 
+        (lateral) of the brain.
+    AP(float): Antero-posterior coordinate. It refers to the position along the anterior-posterior 
+        axis of the brain. The anterior-posterior axis runs from the front (anterior) to the
+        back (posterior) of the brain.
+    DV(float): Dorso-ventral coordinate. It refers to the position along the dorso-ventral axis of
+        the brain. The dorso-ventral axis runs from the top (dorsal) to the bottom (ventral) 
+        of the brain.
+    Returns:
+        str: The constructed URL.
+    """
+    if "ra" in kind.lower():
+        api = "http://labs.gaidi.ca/rat-brain-atlas/api.php?"
+        print(f"check the url: {api[:-8]}?ml={ml}&ap={ap}&dv={dv}")
+    elif "mo" in kind.lower() or "mi" in kind.lower():
+        api = "https://labs.gaidi.ca/mouse-brain-atlas/?"
+    return f"{api}ml={ml}&ap={ap}&dv={dv}"
+
+
+def get_3fpath(dir_save, ml, ap, dv):
+    """
+    Generates a filename based on the provided coordinates and directory.
+
+    Args:
+        dir_save (str): The directory where the file will be saved.
+        ml (float): The ML coordinate.
+        ap (float): The AP coordinate.
+        dv (float): The DV coordinate.
+
+    Returns:
+        str: The generated filename.
+    """
+    filename, file_extension = os.path.splitext(dir_save)
+    if file_extension == "":
+        filename += f"brainatlas_ml={ml}&ap={ap}&dv={dv}"
+    return filename
+
+
+def download_image(image_url, color_mode=True):
+    """
+    Downloads an image from a given URL and converts it to RGB mode if required.
+
+    Args:
+        image_url (str): The URL of the image to download.
+        color_mode (bool, optional): Whether to convert the image to RGB mode. Defaults to True.
+
+    Returns:
+        PIL.Image: The downloaded image.
+    """
+    try:
+        # Download the image from the specified URL
+        response = requests.get(image_url)
+
+        # Check if the response status code is OK (200)
+        response.raise_for_status()
+        image = Image.open(BytesIO(response.content))
+        if color_mode:
+            image = image.convert("RGB")
+        return image
+    except requests.exceptions.RequestException as e:
+        print(f"Error: Unable to download image from {image_url}")
+        print(e)
+        return None
+
+
+def brain_atlas(ml, ap, dv, kind="rat", dir_save=None, pdf_filename=None):
+    """
+    Retrieves images of the rat or mouse brain atlas for the specified coordinates.
+
+    Args:
+        ml (float): The ML coordinate.
+        ap (float): The AP coordinate.
+        dv (float): The DV coordinate.
+        kind (str, optional): The type of brain atlas ('rat' or 'mouse'). Defaults to 'rat'.
+        dir_save (str, optional): The directory where the images will be saved. Defaults to None.
+
+    Returns:
+        tuple: A tuple containing PIL images of coronal, sagittal, and horizontal views, respectively.
+
+    Note:
+        The images are also saved as PDF files in the specified directory if `dir_save` is provided.
+    """
+    # Construct the URL for the rat brain atlas API based on the provided coordinates
+    url = atlas_url(ml, ap, dv, kind=kind)
+    try:
+        response = requests.get(url)
+        response.raise_for_status()
+        data = response.json()
+
+        # Download and process the images from the URLs provided in the JSON data
+        coronal_image = download_image(data["coronal"]["image_url"], color_mode=True)
+        sagittal_image = download_image(data["sagittal"]["image_url"], color_mode=True)
+        horizontal_image = download_image(
+            data["horizontal"]["image_url"], color_mode=True
+        )
+
+        # Check if all images were successfully downloaded
+        if coronal_image and sagittal_image and horizontal_image:
+            if dir_save:
+                # Construct filename with kind suffix
+                filename = get_3fpath(dir_save, ml, ap, dv)
+                coronal_image.save(filename + f"_{kind}_coronal.pdf")
+                sagittal_image.save(filename + f"_{kind}_sagittal.pdf")
+                horizontal_image.save(filename + f"_{kind}_horizontal.pdf")
+            return (coronal_image, sagittal_image, horizontal_image)
+        else:
+            print("Error: Unable to download images.")
+            return None
+    except requests.exceptions.RequestException as e:
+        print(f"Error: Unable to complete web request\n{url}.")
+        print(e)
+        return None
+
+
+# # Example usage:
+# ml = 8.64
+# ap = -0.36
+# dv = 7.0
+
+# # Retrieve the rat brain atlas images for the specified coordinates
+# S = brain_atlas(
+#     ml, ap, dv, dir_save="/Users/macjianfeng/Dropbox/Downloads/", kind="rat"
+# )
+
+# if S:
+#     # Display or further process the retrieved images
+#     coronal_image = S["coronal"]
+#     sagittal_image = S["sagittal"]
+#     horizontal_image = S["horizontal"]
+#     # coronal_image.show()  # Display the coronal image
+#     # Similarly, you can display or process sagittal and horizontal images